Ben Bolstad
| Snapshot Date: 2024-08-14 14:00 -0400 (Wed, 14 Aug 2024) |
| git_url: https://git.bioconductor.org/packages/BufferedMatrix |
| git_branch: devel |
| git_last_commit: d422a05 |
| git_last_commit_date: 2024-04-30 10:16:21 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-08-15 11:41 -0400 (Thu, 15 Aug 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4420 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4413 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 249/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BufferedMatrix 1.69.0 (landing page) Ben Bolstad
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the BufferedMatrix package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BufferedMatrix.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BufferedMatrix |
| Version: 1.69.0 |
| Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BufferedMatrix.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BufferedMatrix_1.69.0.tar.gz |
| StartedAt: 2024-08-14 22:51:37 -0400 (Wed, 14 Aug 2024) |
| EndedAt: 2024-08-14 22:54:18 -0400 (Wed, 14 Aug 2024) |
| EllapsedTime: 161.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BufferedMatrix.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BufferedMatrix.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BufferedMatrix_1.69.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'BufferedMatrix/DESCRIPTION' ... OK
* this is package 'BufferedMatrix' version '1.69.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'BufferedMatrix' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 13.2.0'
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) BufferedMatrix-class.Rd:209: Lost braces; missing escapes or markup?
209 | $x^{power}$ elementwise of the matrix
| ^
prepare_Rd: createBufferedMatrix.Rd:26: Dropping empty section \keyword
prepare_Rd: createBufferedMatrix.Rd:17-18: Dropping empty section \details
prepare_Rd: createBufferedMatrix.Rd:15-16: Dropping empty section \value
prepare_Rd: createBufferedMatrix.Rd:19-20: Dropping empty section \references
prepare_Rd: createBufferedMatrix.Rd:21-22: Dropping empty section \seealso
prepare_Rd: createBufferedMatrix.Rd:23-24: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.20-bioc/R/library/BufferedMatrix/libs/x64/BufferedMatrix.dll':
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... NONE
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'Rcodetesting.R'
Running 'c_code_level_tests.R'
Running 'objectTesting.R'
Running 'rawCalltesting.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
'F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/00check.log'
for details.
BufferedMatrix.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL BufferedMatrix
###
##############################################################################
##############################################################################
* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'BufferedMatrix' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RBufferedMatrix.c -o RBufferedMatrix.o
gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c doubleBufferedMatrix.c -o doubleBufferedMatrix.o
doubleBufferedMatrix.c: In function 'dbm_ReadOnlyMode':
doubleBufferedMatrix.c:1580:7: warning: suggest parentheses around operand of '!' or change '&' to '&&' or '!' to '~' [-Wparentheses]
1580 | if (!(Matrix->readonly) & setting){
| ^~~~~~~~~~~~~~~~~~~
doubleBufferedMatrix.c: At top level:
doubleBufferedMatrix.c:3327:12: warning: 'sort_double' defined but not used [-Wunused-function]
3327 | static int sort_double(const double *a1,const double *a2){
| ^~~~~~~~~~~
gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c doubleBufferedMatrix_C_tests.c -o doubleBufferedMatrix_C_tests.o
gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c init_package.c -o init_package.o
gcc -shared -s -static-libgcc -o BufferedMatrix.dll tmp.def RBufferedMatrix.o doubleBufferedMatrix.o doubleBufferedMatrix_C_tests.o init_package.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-BufferedMatrix/00new/BufferedMatrix/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'rowMeans' in package 'BufferedMatrix'
Creating a new generic function for 'rowSums' in package 'BufferedMatrix'
Creating a new generic function for 'colMeans' in package 'BufferedMatrix'
Creating a new generic function for 'colSums' in package 'BufferedMatrix'
Creating a generic function for 'ncol' from package 'base' in package 'BufferedMatrix'
Creating a generic function for 'nrow' from package 'base' in package 'BufferedMatrix'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BufferedMatrix)
BufferedMatrix.Rcheck/tests/c_code_level_tests.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix", "BufferedMatrix", .libPaths());.C("dbm_c_tester",integer(1))
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
Adding Additional Column
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 1
Buffer Cols: 1
0.000000 1.000000 2.000000 3.000000 4.000000 0.000000
1.000000 2.000000 3.000000 4.000000 5.000000 0.000000
2.000000 3.000000 4.000000 5.000000 6.000000 0.000000
3.000000 4.000000 5.000000 6.000000 7.000000 0.000000
4.000000 5.000000 6.000000 7.000000 8.000000 0.000000
Reassigning values
1.000000 6.000000 11.000000 16.000000 21.000000 26.000000
2.000000 7.000000 12.000000 17.000000 22.000000 27.000000
3.000000 8.000000 13.000000 18.000000 23.000000 28.000000
4.000000 9.000000 14.000000 19.000000 24.000000 29.000000
5.000000 10.000000 15.000000 20.000000 25.000000 30.000000
Resizing Buffers
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 3
Buffer Cols: 3
1.000000 6.000000 11.000000 16.000000 21.000000 26.000000
2.000000 7.000000 12.000000 17.000000 22.000000 27.000000
3.000000 8.000000 13.000000 18.000000 23.000000 28.000000
4.000000 9.000000 14.000000 19.000000 24.000000 29.000000
5.000000 10.000000 15.000000 20.000000 25.000000 30.000000
Activating Row Buffer
In row mode: 1
1.000000 6.000000 11.000000 16.000000 21.000000 26.000000
2.000000 7.000000 12.000000 17.000000 22.000000 27.000000
3.000000 8.000000 13.000000 18.000000 23.000000 28.000000
4.000000 9.000000 14.000000 19.000000 24.000000 29.000000
5.000000 10.000000 15.000000 20.000000 25.000000 30.000000
Squaring Last Column
1.000000 6.000000 11.000000 16.000000 21.000000 676.000000
2.000000 7.000000 12.000000 17.000000 22.000000 729.000000
3.000000 8.000000 13.000000 18.000000 23.000000 784.000000
4.000000 9.000000 14.000000 19.000000 24.000000 841.000000
5.000000 10.000000 15.000000 20.000000 25.000000 900.000000
Square rooting Last Row, then turing off Row Buffer
In row mode: 0
Checking on value that should be not be in column buffer2.236068
1.000000 6.000000 11.000000 16.000000 21.000000 676.000000
2.000000 7.000000 12.000000 17.000000 22.000000 729.000000
3.000000 8.000000 13.000000 18.000000 23.000000 784.000000
4.000000 9.000000 14.000000 19.000000 24.000000 841.000000
2.236068 3.162278 3.872983 4.472136 5.000000 30.000000
Single Indexing. Assign each value its square
1.000000 36.000000 121.000000 256.000000 441.000000 676.000000
4.000000 49.000000 144.000000 289.000000 484.000000 729.000000
9.000000 64.000000 169.000000 324.000000 529.000000 784.000000
16.000000 81.000000 196.000000 361.000000 576.000000 841.000000
25.000000 100.000000 225.000000 400.000000 625.000000 900.000000
Resizing Buffers Smaller
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 1
Buffer Cols: 1
1.000000 36.000000 121.000000 256.000000 441.000000 676.000000
4.000000 49.000000 144.000000 289.000000 484.000000 729.000000
9.000000 64.000000 169.000000 324.000000 529.000000 784.000000
16.000000 81.000000 196.000000 361.000000 576.000000 841.000000
25.000000 100.000000 225.000000 400.000000 625.000000 900.000000
Activating Row Mode.
Resizing Buffers
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 1
Buffer Cols: 1
Activating ReadOnly Mode.
The results of assignment is: 0
Printing matrix reversed.
900.000000 625.000000 400.000000 225.000000 100.000000 25.000000
841.000000 576.000000 361.000000 196.000000 81.000000 16.000000
784.000000 529.000000 324.000000 169.000000 64.000000 9.000000
729.000000 484.000000 289.000000 144.000000 49.000000 -30.000000
676.000000 441.000000 256.000000 121.000000 -20.000000 -10.000000
[[1]]
[1] 0
>
> proc.time()
user system elapsed
0.35 0.31 1.34
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths());
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
>
>
> ### this is used to control how many repetitions in something below
> ### higher values result in more checks.
> nreps <-100 ##20000
>
>
> ## test creation and some simple assignments and subsetting operations
>
> ## first on single elements
> tmp <- createBufferedMatrix(1000,10)
>
> tmp[10,5]
[1] 0
> tmp[10,5] <- 10
> tmp[10,5]
[1] 10
> tmp[10,5] <- 12.445
> tmp[10,5]
[1] 12.445
>
>
>
> ## now testing accessing multiple elements
> tmp2 <- createBufferedMatrix(10,20)
>
>
> tmp2[3,1] <- 51.34
> tmp2[9,2] <- 9.87654
> tmp2[,1:2]
[,1] [,2]
[1,] 0.00 0.00000
[2,] 0.00 0.00000
[3,] 51.34 0.00000
[4,] 0.00 0.00000
[5,] 0.00 0.00000
[6,] 0.00 0.00000
[7,] 0.00 0.00000
[8,] 0.00 0.00000
[9,] 0.00 9.87654
[10,] 0.00 0.00000
> tmp2[,-(3:20)]
[,1] [,2]
[1,] 0.00 0.00000
[2,] 0.00 0.00000
[3,] 51.34 0.00000
[4,] 0.00 0.00000
[5,] 0.00 0.00000
[6,] 0.00 0.00000
[7,] 0.00 0.00000
[8,] 0.00 0.00000
[9,] 0.00 9.87654
[10,] 0.00 0.00000
> tmp2[3,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 51.34 0 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
[1,] 0 0 0 0 0 0 0
> tmp2[-3,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[2,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[3,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[4,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[5,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[6,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[7,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[8,] 0 9.87654 0 0 0 0 0 0 0 0 0 0 0
[9,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
[1,] 0 0 0 0 0 0 0
[2,] 0 0 0 0 0 0 0
[3,] 0 0 0 0 0 0 0
[4,] 0 0 0 0 0 0 0
[5,] 0 0 0 0 0 0 0
[6,] 0 0 0 0 0 0 0
[7,] 0 0 0 0 0 0 0
[8,] 0 0 0 0 0 0 0
[9,] 0 0 0 0 0 0 0
> tmp2[2,1:3]
[,1] [,2] [,3]
[1,] 0 0 0
> tmp2[3:9,1:3]
[,1] [,2] [,3]
[1,] 51.34 0.00000 0
[2,] 0.00 0.00000 0
[3,] 0.00 0.00000 0
[4,] 0.00 0.00000 0
[5,] 0.00 0.00000 0
[6,] 0.00 0.00000 0
[7,] 0.00 9.87654 0
> tmp2[-4,-4]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[2,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[3,] 51.34 0.00000 0 0 0 0 0 0 0 0 0 0 0
[4,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[5,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[6,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[7,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[8,] 0.00 9.87654 0 0 0 0 0 0 0 0 0 0 0
[9,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19]
[1,] 0 0 0 0 0 0
[2,] 0 0 0 0 0 0
[3,] 0 0 0 0 0 0
[4,] 0 0 0 0 0 0
[5,] 0 0 0 0 0 0
[6,] 0 0 0 0 0 0
[7,] 0 0 0 0 0 0
[8,] 0 0 0 0 0 0
[9,] 0 0 0 0 0 0
>
> ## now testing accessing/assigning multiple elements
> tmp3 <- createBufferedMatrix(10,10)
>
> for (i in 1:10){
+ for (j in 1:10){
+ tmp3[i,j] <- (j-1)*10 + i
+ }
+ }
>
> tmp3[2:4,2:4]
[,1] [,2] [,3]
[1,] 12 22 32
[2,] 13 23 33
[3,] 14 24 34
> tmp3[c(-10),c(2:4,2:4,10,1,2,1:10,10:1)]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 11 21 31 11 21 31 91 1 11 1 11 21 31
[2,] 12 22 32 12 22 32 92 2 12 2 12 22 32
[3,] 13 23 33 13 23 33 93 3 13 3 13 23 33
[4,] 14 24 34 14 24 34 94 4 14 4 14 24 34
[5,] 15 25 35 15 25 35 95 5 15 5 15 25 35
[6,] 16 26 36 16 26 36 96 6 16 6 16 26 36
[7,] 17 27 37 17 27 37 97 7 17 7 17 27 37
[8,] 18 28 38 18 28 38 98 8 18 8 18 28 38
[9,] 19 29 39 19 29 39 99 9 19 9 19 29 39
[,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25]
[1,] 41 51 61 71 81 91 91 81 71 61 51 41
[2,] 42 52 62 72 82 92 92 82 72 62 52 42
[3,] 43 53 63 73 83 93 93 83 73 63 53 43
[4,] 44 54 64 74 84 94 94 84 74 64 54 44
[5,] 45 55 65 75 85 95 95 85 75 65 55 45
[6,] 46 56 66 76 86 96 96 86 76 66 56 46
[7,] 47 57 67 77 87 97 97 87 77 67 57 47
[8,] 48 58 68 78 88 98 98 88 78 68 58 48
[9,] 49 59 69 79 89 99 99 89 79 69 59 49
[,26] [,27] [,28] [,29]
[1,] 31 21 11 1
[2,] 32 22 12 2
[3,] 33 23 13 3
[4,] 34 24 14 4
[5,] 35 25 15 5
[6,] 36 26 16 6
[7,] 37 27 17 7
[8,] 38 28 18 8
[9,] 39 29 19 9
> tmp3[-c(1:5),-c(6:10)]
[,1] [,2] [,3] [,4] [,5]
[1,] 6 16 26 36 46
[2,] 7 17 27 37 47
[3,] 8 18 28 38 48
[4,] 9 19 29 39 49
[5,] 10 20 30 40 50
>
> ## assignment of whole columns
> tmp3[,1] <- c(1:10*100.0)
> tmp3[,1:2] <- tmp3[,1:2]*100
> tmp3[,1:2] <- tmp3[,2:1]
> tmp3[,1:2]
[,1] [,2]
[1,] 1100 1e+04
[2,] 1200 2e+04
[3,] 1300 3e+04
[4,] 1400 4e+04
[5,] 1500 5e+04
[6,] 1600 6e+04
[7,] 1700 7e+04
[8,] 1800 8e+04
[9,] 1900 9e+04
[10,] 2000 1e+05
>
>
> tmp3[,-1] <- tmp3[,1:9]
> tmp3[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1100 1100 1e+04 21 31 41 51 61 71 81
[2,] 1200 1200 2e+04 22 32 42 52 62 72 82
[3,] 1300 1300 3e+04 23 33 43 53 63 73 83
[4,] 1400 1400 4e+04 24 34 44 54 64 74 84
[5,] 1500 1500 5e+04 25 35 45 55 65 75 85
[6,] 1600 1600 6e+04 26 36 46 56 66 76 86
[7,] 1700 1700 7e+04 27 37 47 57 67 77 87
[8,] 1800 1800 8e+04 28 38 48 58 68 78 88
[9,] 1900 1900 9e+04 29 39 49 59 69 79 89
[10,] 2000 2000 1e+05 30 40 50 60 70 80 90
>
> tmp3[,1:2] <- rep(1,10)
> tmp3[,1:2] <- rep(1,20)
> tmp3[,1:2] <- matrix(c(1:5),1,5)
>
> tmp3[,-c(1:8)] <- matrix(c(1:5),1,5)
>
> tmp3[1,] <- 1:10
> tmp3[1,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
> tmp3[-1,] <- c(1,2)
> tmp3[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
[2,] 1 2 1 2 1 2 1 2 1 2
[3,] 2 1 2 1 2 1 2 1 2 1
[4,] 1 2 1 2 1 2 1 2 1 2
[5,] 2 1 2 1 2 1 2 1 2 1
[6,] 1 2 1 2 1 2 1 2 1 2
[7,] 2 1 2 1 2 1 2 1 2 1
[8,] 1 2 1 2 1 2 1 2 1 2
[9,] 2 1 2 1 2 1 2 1 2 1
[10,] 1 2 1 2 1 2 1 2 1 2
> tmp3[-c(1:8),] <- matrix(c(1:5),1,5)
> tmp3[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
[2,] 1 2 1 2 1 2 1 2 1 2
[3,] 2 1 2 1 2 1 2 1 2 1
[4,] 1 2 1 2 1 2 1 2 1 2
[5,] 2 1 2 1 2 1 2 1 2 1
[6,] 1 2 1 2 1 2 1 2 1 2
[7,] 2 1 2 1 2 1 2 1 2 1
[8,] 1 2 1 2 1 2 1 2 1 2
[9,] 1 3 5 2 4 1 3 5 2 4
[10,] 2 4 1 3 5 2 4 1 3 5
>
>
> tmp3[1:2,1:2] <- 5555.04
> tmp3[-(1:2),1:2] <- 1234.56789
>
>
>
> ## testing accessors for the directory and prefix
> directory(tmp3)
[1] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests"
> prefix(tmp3)
[1] "BM"
>
> ## testing if we can remove these objects
> rm(tmp, tmp2, tmp3)
> gc()
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 468463 25.1 1021760 54.6 633411 33.9
Vcells 853871 6.6 8388608 64.0 2003095 15.3
>
>
>
>
> ##
> ## checking reads
> ##
>
> tmp2 <- createBufferedMatrix(10,20)
>
> test.sample <- rnorm(10*20)
>
> tmp2[1:10,1:20] <- test.sample
>
> test.matrix <- matrix(test.sample,10,20)
>
> ## testing reads
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ which.col <- sample(1:20,1)
+ if (tmp2[which.row,which.col] != test.matrix[which.row,which.col]){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> date()
[1] "Wed Aug 14 22:52:11 2024"
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
> date()
[1] "Wed Aug 14 22:52:13 2024"
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,which.col] == test.matrix[which.row,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
>
>
> RowMode(tmp2)
<pointer: 0x000002cf124ff8f0>
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ which.col <- sample(1:20,1)
+ if (tmp2[which.row,which.col] != test.matrix[which.row,which.col]){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,5,replace=TRUE)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> date()
[1] "Wed Aug 14 22:52:45 2024"
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:20,5,replace=TRUE)
+ if (!all(tmp2[which.row,which.col] == test.matrix[which.row,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
> date()
[1] "Wed Aug 14 22:52:56 2024"
>
> ColMode(tmp2)
<pointer: 0x000002cf124ff8f0>
>
>
>
> ### Now testing assignments
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+
+ new.data <- rnorm(20)
+ tmp2[which.row,] <- new.data
+ test.matrix[which.row,] <- new.data
+ if (rep > 1){
+ if (!all(tmp2[prev.row,] == test.matrix[prev.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ new.data <- rnorm(10)
+ tmp2[,which.col] <- new.data
+ test.matrix[,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[,prev.col] == test.matrix[,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.col <- which.col
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,5,replace=TRUE)
+ new.data <- matrix(rnorm(50),5,10)
+ tmp2[,which.col] <- new.data
+ test.matrix[,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[,prev.col] == test.matrix[,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.col <- which.col
+ }
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ new.data <- matrix(rnorm(50),5,10)
+ tmp2[which.row,] <- new.data
+ test.matrix[which.row,]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[prev.row,] == test.matrix[prev.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:20,5,replace=TRUE)
+ new.data <- matrix(rnorm(25),5,5)
+ tmp2[which.row,which.col] <- new.data
+ test.matrix[which.row,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[prev.row,prev.col] == test.matrix[prev.row,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+ prev.col <- which.col
+ }
>
>
>
>
> ###
> ###
> ### testing some more functions
> ###
>
>
>
> ## duplication function
> tmp5 <- duplicate(tmp2)
>
> # making sure really did copy everything.
> tmp5[1,1] <- tmp5[1,1] +100.00
>
> if (tmp5[1,1] == tmp2[1,1]){
+ stop("Problem with duplication")
+ }
>
>
>
>
> ### testing elementwise applying of functions
>
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 99.6144646 3.0014403 0.1870207 0.9384668
[2,] 1.3204737 -2.0481167 -0.3310702 1.2748685
[3,] -0.3416812 1.5520175 1.2694945 -0.6554801
[4,] 1.2389287 0.1190015 0.3978675 0.6652192
> ewApply(tmp5,abs)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 99.6144646 3.0014403 0.1870207 0.9384668
[2,] 1.3204737 2.0481167 0.3310702 1.2748685
[3,] 0.3416812 1.5520175 1.2694945 0.6554801
[4,] 1.2389287 0.1190015 0.3978675 0.6652192
> ewApply(tmp5,sqrt)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 9.980705 1.732467 0.4324589 0.9687450
[2,] 1.149119 1.431124 0.5753870 1.1291007
[3,] 0.584535 1.245800 1.1267185 0.8096173
[4,] 1.113072 0.344966 0.6307674 0.8156097
>
> my.function <- function(x,power){
+ (x+5)^power
+ }
>
> ewApply(tmp5,my.function,power=2)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 224.42151 45.32611 29.51161 35.62592
[2,] 37.81166 41.35936 31.08494 37.56588
[3,] 31.18703 39.01002 37.53668 33.75165
[4,] 37.36965 28.56866 31.70554 33.82132
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x000002cf124ffa10>
> exp(tmp5)
<pointer: 0x000002cf124ffa10>
> log(tmp5,2)
<pointer: 0x000002cf124ffa10>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 467.104
> Min(tmp5)
[1] 53.27808
> mean(tmp5)
[1] 73.65157
> Sum(tmp5)
[1] 14730.31
> Var(tmp5)
[1] 863.4754
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 92.41901 71.06020 74.23962 72.30170 69.33065 72.55288 70.37917 73.42348
[9] 72.20571 68.60323
> rowSums(tmp5)
[1] 1848.380 1421.204 1484.792 1446.034 1386.613 1451.058 1407.583 1468.470
[9] 1444.114 1372.065
> rowVars(tmp5)
[1] 7862.16209 65.39750 97.81625 59.36969 32.65071 105.76874
[7] 128.10533 91.68468 89.30087 70.12942
> rowSd(tmp5)
[1] 88.668834 8.086872 9.890210 7.705173 5.714080 10.284393 11.318362
[8] 9.575212 9.449914 8.374331
> rowMax(tmp5)
[1] 467.10397 86.33656 90.61629 91.00232 79.58999 89.33192 91.27256
[8] 90.27378 88.55183 84.69909
> rowMin(tmp5)
[1] 56.99484 61.07557 56.94369 59.17122 55.11731 53.87727 53.82002 55.07683
[9] 53.27808 55.41406
>
> colMeans(tmp5)
[1] 111.98587 73.15001 69.38056 70.93075 69.77342 70.31447 71.14466
[8] 72.42316 75.20264 74.12828 71.95502 72.27001 67.97824 70.88337
[15] 71.38981 68.11567 73.27517 72.67218 72.47361 73.58443
> colSums(tmp5)
[1] 1119.8587 731.5001 693.8056 709.3075 697.7342 703.1447 711.4466
[8] 724.2316 752.0264 741.2828 719.5502 722.7001 679.7824 708.8337
[15] 713.8981 681.1567 732.7517 726.7218 724.7361 735.8443
> colVars(tmp5)
[1] 15615.27286 194.90361 37.92177 97.41307 57.54830 99.27365
[7] 82.17952 41.25711 54.20897 19.87117 98.34915 86.93198
[13] 63.59959 131.76373 85.57348 70.62451 118.63102 201.71734
[19] 52.69105 88.32604
> colSd(tmp5)
[1] 124.961085 13.960788 6.158065 9.869806 7.586060 9.963616
[7] 9.065292 6.423170 7.362674 4.457710 9.917114 9.323732
[13] 7.974935 11.478838 9.250594 8.403839 10.891787 14.202723
[19] 7.258860 9.398193
> colMax(tmp5)
[1] 467.10397 94.34035 78.12768 83.27584 82.53619 82.22571 83.55414
[8] 83.35733 87.69423 79.58999 91.27256 91.00232 80.29358 90.12611
[15] 86.33656 84.39956 90.27378 90.61629 84.27697 86.75665
> colMin(tmp5)
[1] 59.80413 55.07683 61.42455 55.11731 57.61658 53.27808 58.87079 63.29021
[9] 62.28398 66.44260 56.23874 56.94369 56.99484 53.82002 61.86835 57.95206
[17] 61.84811 54.68088 62.83565 61.13318
>
>
> ### setting a random element to NA and then testing with na.rm=TRUE or na.rm=FALSE (The default)
>
>
> which.row <- sample(1:10,1,replace=TRUE)
> which.col <- sample(1:20,1,replace=TRUE)
>
> tmp5[which.row,which.col] <- NA
>
> Max(tmp5)
[1] NA
> Min(tmp5)
[1] NA
> mean(tmp5)
[1] NA
> Sum(tmp5)
[1] NA
> Var(tmp5)
[1] NA
>
> rowMeans(tmp5)
[1] 92.41901 NA 74.23962 72.30170 69.33065 72.55288 70.37917 73.42348
[9] 72.20571 68.60323
> rowSums(tmp5)
[1] 1848.380 NA 1484.792 1446.034 1386.613 1451.058 1407.583 1468.470
[9] 1444.114 1372.065
> rowVars(tmp5)
[1] 7862.16209 63.20071 97.81625 59.36969 32.65071 105.76874
[7] 128.10533 91.68468 89.30087 70.12942
> rowSd(tmp5)
[1] 88.668834 7.949887 9.890210 7.705173 5.714080 10.284393 11.318362
[8] 9.575212 9.449914 8.374331
> rowMax(tmp5)
[1] 467.10397 NA 90.61629 91.00232 79.58999 89.33192 91.27256
[8] 90.27378 88.55183 84.69909
> rowMin(tmp5)
[1] 56.99484 NA 56.94369 59.17122 55.11731 53.87727 53.82002 55.07683
[9] 53.27808 55.41406
>
> colMeans(tmp5)
[1] 111.98587 73.15001 69.38056 70.93075 69.77342 70.31447 71.14466
[8] 72.42316 75.20264 74.12828 NA 72.27001 67.97824 70.88337
[15] 71.38981 68.11567 73.27517 72.67218 72.47361 73.58443
> colSums(tmp5)
[1] 1119.8587 731.5001 693.8056 709.3075 697.7342 703.1447 711.4466
[8] 724.2316 752.0264 741.2828 NA 722.7001 679.7824 708.8337
[15] 713.8981 681.1567 732.7517 726.7218 724.7361 735.8443
> colVars(tmp5)
[1] 15615.27286 194.90361 37.92177 97.41307 57.54830 99.27365
[7] 82.17952 41.25711 54.20897 19.87117 NA 86.93198
[13] 63.59959 131.76373 85.57348 70.62451 118.63102 201.71734
[19] 52.69105 88.32604
> colSd(tmp5)
[1] 124.961085 13.960788 6.158065 9.869806 7.586060 9.963616
[7] 9.065292 6.423170 7.362674 4.457710 NA 9.323732
[13] 7.974935 11.478838 9.250594 8.403839 10.891787 14.202723
[19] 7.258860 9.398193
> colMax(tmp5)
[1] 467.10397 94.34035 78.12768 83.27584 82.53619 82.22571 83.55414
[8] 83.35733 87.69423 79.58999 NA 91.00232 80.29358 90.12611
[15] 86.33656 84.39956 90.27378 90.61629 84.27697 86.75665
> colMin(tmp5)
[1] 59.80413 55.07683 61.42455 55.11731 57.61658 53.27808 58.87079 63.29021
[9] 62.28398 66.44260 NA 56.94369 56.99484 53.82002 61.86835 57.95206
[17] 61.84811 54.68088 62.83565 61.13318
>
> Max(tmp5,na.rm=TRUE)
[1] 467.104
> Min(tmp5,na.rm=TRUE)
[1] 53.27808
> mean(tmp5,na.rm=TRUE)
[1] 73.71476
> Sum(tmp5,na.rm=TRUE)
[1] 14669.24
> Var(tmp5,na.rm=TRUE)
[1] 867.0336
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 92.41901 71.58571 74.23962 72.30170 69.33065 72.55288 70.37917 73.42348
[9] 72.20571 68.60323
> rowSums(tmp5,na.rm=TRUE)
[1] 1848.380 1360.128 1484.792 1446.034 1386.613 1451.058 1407.583 1468.470
[9] 1444.114 1372.065
> rowVars(tmp5,na.rm=TRUE)
[1] 7862.16209 63.20071 97.81625 59.36969 32.65071 105.76874
[7] 128.10533 91.68468 89.30087 70.12942
> rowSd(tmp5,na.rm=TRUE)
[1] 88.668834 7.949887 9.890210 7.705173 5.714080 10.284393 11.318362
[8] 9.575212 9.449914 8.374331
> rowMax(tmp5,na.rm=TRUE)
[1] 467.10397 86.33656 90.61629 91.00232 79.58999 89.33192 91.27256
[8] 90.27378 88.55183 84.69909
> rowMin(tmp5,na.rm=TRUE)
[1] 56.99484 61.84811 56.94369 59.17122 55.11731 53.87727 53.82002 55.07683
[9] 53.27808 55.41406
>
> colMeans(tmp5,na.rm=TRUE)
[1] 111.98587 73.15001 69.38056 70.93075 69.77342 70.31447 71.14466
[8] 72.42316 75.20264 74.12828 73.16385 72.27001 67.97824 70.88337
[15] 71.38981 68.11567 73.27517 72.67218 72.47361 73.58443
> colSums(tmp5,na.rm=TRUE)
[1] 1119.8587 731.5001 693.8056 709.3075 697.7342 703.1447 711.4466
[8] 724.2316 752.0264 741.2828 658.4746 722.7001 679.7824 708.8337
[15] 713.8981 681.1567 732.7517 726.7218 724.7361 735.8443
> colVars(tmp5,na.rm=TRUE)
[1] 15615.27286 194.90361 37.92177 97.41307 57.54830 99.27365
[7] 82.17952 41.25711 54.20897 19.87117 94.20358 86.93198
[13] 63.59959 131.76373 85.57348 70.62451 118.63102 201.71734
[19] 52.69105 88.32604
> colSd(tmp5,na.rm=TRUE)
[1] 124.961085 13.960788 6.158065 9.869806 7.586060 9.963616
[7] 9.065292 6.423170 7.362674 4.457710 9.705853 9.323732
[13] 7.974935 11.478838 9.250594 8.403839 10.891787 14.202723
[19] 7.258860 9.398193
> colMax(tmp5,na.rm=TRUE)
[1] 467.10397 94.34035 78.12768 83.27584 82.53619 82.22571 83.55414
[8] 83.35733 87.69423 79.58999 91.27256 91.00232 80.29358 90.12611
[15] 86.33656 84.39956 90.27378 90.61629 84.27697 86.75665
> colMin(tmp5,na.rm=TRUE)
[1] 59.80413 55.07683 61.42455 55.11731 57.61658 53.27808 58.87079 63.29021
[9] 62.28398 66.44260 56.23874 56.94369 56.99484 53.82002 61.86835 57.95206
[17] 61.84811 54.68088 62.83565 61.13318
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 92.41901 NaN 74.23962 72.30170 69.33065 72.55288 70.37917 73.42348
[9] 72.20571 68.60323
> rowSums(tmp5,na.rm=TRUE)
[1] 1848.380 0.000 1484.792 1446.034 1386.613 1451.058 1407.583 1468.470
[9] 1444.114 1372.065
> rowVars(tmp5,na.rm=TRUE)
[1] 7862.16209 NA 97.81625 59.36969 32.65071 105.76874
[7] 128.10533 91.68468 89.30087 70.12942
> rowSd(tmp5,na.rm=TRUE)
[1] 88.668834 NA 9.890210 7.705173 5.714080 10.284393 11.318362
[8] 9.575212 9.449914 8.374331
> rowMax(tmp5,na.rm=TRUE)
[1] 467.10397 NA 90.61629 91.00232 79.58999 89.33192 91.27256
[8] 90.27378 88.55183 84.69909
> rowMin(tmp5,na.rm=TRUE)
[1] 56.99484 NA 56.94369 59.17122 55.11731 53.87727 53.82002 55.07683
[9] 53.27808 55.41406
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 115.68430 71.71289 69.90071 70.12434 69.97806 68.99100 71.75552
[8] 73.43793 75.09493 73.85483 NaN 72.36408 67.44364 71.30406
[15] 69.72906 68.06814 74.54485 73.63270 73.48282 74.52220
> colSums(tmp5,na.rm=TRUE)
[1] 1041.1587 645.4160 629.1064 631.1190 629.8026 620.9190 645.7997
[8] 660.9414 675.8544 664.6935 0.0000 651.2767 606.9928 641.7365
[15] 627.5615 612.6133 670.9036 662.6943 661.3453 670.6998
> colVars(tmp5,na.rm=TRUE)
[1] 17413.30032 196.03178 39.61826 102.27383 64.27070 91.97761
[7] 88.25408 34.82941 60.85459 21.51388 NA 97.69891
[13] 68.33436 146.24313 65.24165 79.42716 115.32407 216.55277
[19] 47.81929 89.47333
> colSd(tmp5,na.rm=TRUE)
[1] 131.959465 14.001135 6.294304 10.113053 8.016901 9.590496
[7] 9.394364 5.901645 7.800935 4.638306 NA 9.884276
[13] 8.266460 12.093103 8.077231 8.912192 10.738905 14.715732
[19] 6.915149 9.459034
> colMax(tmp5,na.rm=TRUE)
[1] 467.10397 94.34035 78.12768 83.27584 82.53619 77.96534 83.55414
[8] 83.35733 87.69423 79.58999 -Inf 91.00232 80.29358 90.12611
[15] 85.30363 84.39956 90.27378 90.61629 84.27697 86.75665
> colMin(tmp5,na.rm=TRUE)
[1] 59.80413 55.07683 61.42455 55.11731 57.61658 53.27808 58.87079 67.08512
[9] 62.28398 66.44260 Inf 56.94369 56.99484 53.82002 61.86835 57.95206
[17] 62.77904 54.68088 62.83565 61.13318
>
>
>
>
> copymatrix <- matrix(rnorm(200,150,15),10,20)
>
> tmp5[1:10,1:20] <- copymatrix
> which.row <- 3
> which.col <- 1
> cat(which.row," ",which.col,"\n")
3 1
> tmp5[which.row,which.col] <- NA
> copymatrix[which.row,which.col] <- NA
>
> rowVars(tmp5,na.rm=TRUE)
[1] 306.9430 279.0321 356.9567 123.0352 220.0614 210.7713 349.3557 311.6808
[9] 376.1124 306.1938
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 306.9430 279.0321 356.9567 123.0352 220.0614 210.7713 349.3557 311.6808
[9] 376.1124 306.1938
>
>
>
> copymatrix <- matrix(rnorm(200,150,15),10,20)
>
> tmp5[1:10,1:20] <- copymatrix
> which.row <- 1
> which.col <- 3
> cat(which.row," ",which.col,"\n")
1 3
> tmp5[which.row,which.col] <- NA
> copymatrix[which.row,which.col] <- NA
>
> colVars(tmp5,na.rm=TRUE)-apply(copymatrix,2,var,na.rm=TRUE)
[1] -1.989520e-13 -5.684342e-14 -5.684342e-14 2.273737e-13 1.136868e-13
[6] -5.684342e-14 -7.105427e-14 -2.842171e-14 -5.684342e-14 0.000000e+00
[11] 1.136868e-13 0.000000e+00 -5.684342e-14 5.684342e-14 -2.273737e-13
[16] -5.684342e-14 8.526513e-14 2.842171e-14 1.136868e-13 1.136868e-13
>
>
>
>
>
>
>
>
>
>
> ## making sure these things agree
> ##
> ## first when there is no NA
>
>
>
> agree.checks <- function(buff.matrix,r.matrix,err.tol=1e-10){
+
+ if (Max(buff.matrix,na.rm=TRUE) != max(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Max")
+ }
+
+
+ if (Min(buff.matrix,na.rm=TRUE) != min(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Min")
+ }
+
+
+ if (abs(Sum(buff.matrix,na.rm=TRUE)- sum(r.matrix,na.rm=TRUE)) > err.tol){
+
+ cat(Sum(buff.matrix,na.rm=TRUE),"\n")
+ cat(sum(r.matrix,na.rm=TRUE),"\n")
+ cat(Sum(buff.matrix,na.rm=TRUE) - sum(r.matrix,na.rm=TRUE),"\n")
+
+ stop("No agreement in Sum")
+ }
+
+ if (abs(mean(buff.matrix,na.rm=TRUE) - mean(r.matrix,na.rm=TRUE)) > err.tol){
+ stop("No agreement in mean")
+ }
+
+
+ if(abs(Var(buff.matrix,na.rm=TRUE) - var(as.vector(r.matrix),na.rm=TRUE)) > err.tol){
+ stop("No agreement in Var")
+ }
+
+
+
+ if(any(abs(rowMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,mean,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowMeans")
+ }
+
+
+ if(any(abs(colMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,mean,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colMeans")
+ }
+
+
+ if(any(abs(rowSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in rowSums")
+ }
+
+
+ if(any(abs(colSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colSums")
+ }
+
+ ### this is to get around the fact that R doesn't like to compute NA on an entire vector of NA when
+ ### computing variance
+ my.Var <- function(x,na.rm=FALSE){
+ if (all(is.na(x))){
+ return(NA)
+ } else {
+ var(x,na.rm=na.rm)
+ }
+
+ }
+
+ if(any(abs(rowVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(colVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(rowMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+ if(any(abs(colMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+
+ if(any(abs(rowMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+
+ if(any(abs(colMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+ if(any(abs(colMedians(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,median,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMedian")
+ }
+
+ if(any(abs(colRanges(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,range,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colRanges")
+ }
+
+
+
+ }
>
>
>
>
>
>
>
>
>
> for (rep in 1:20){
+ copymatrix <- matrix(rnorm(200,150,15),10,20)
+
+ tmp5[1:10,1:20] <- copymatrix
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ## now lets assign some NA values and check agreement
+
+ which.row <- sample(1:10,1,replace=TRUE)
+ which.col <- sample(1:20,1,replace=TRUE)
+
+ cat(which.row," ",which.col,"\n")
+
+ tmp5[which.row,which.col] <- NA
+ copymatrix[which.row,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ## make an entire row NA
+ tmp5[which.row,] <- NA
+ copymatrix[which.row,] <- NA
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ### also make an entire col NA
+ tmp5[,which.col] <- NA
+ copymatrix[,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ### now make 1 element non NA with NA in the rest of row and column
+
+ tmp5[which.row,which.col] <- rnorm(1,150,15)
+ copymatrix[which.row,which.col] <- tmp5[which.row,which.col]
+
+ agree.checks(tmp5,copymatrix)
+ }
10 13
3 10
8 14
7 15
9 11
5 19
9 20
7 16
7 3
10 19
5 6
8 10
7 13
4 12
10 19
3 11
8 16
2 20
5 18
10 5
There were 50 or more warnings (use warnings() to see the first 50)
>
>
> ### now test 1 by n and n by 1 matrix
>
>
> err.tol <- 1e-12
>
> rm(tmp5)
>
> dataset1 <- rnorm(100)
> dataset2 <- rnorm(100)
>
> tmp <- createBufferedMatrix(1,100)
> tmp[1,] <- dataset1
>
> tmp2 <- createBufferedMatrix(100,1)
> tmp2[,1] <- dataset2
>
>
>
>
>
> Max(tmp)
[1] 2.431375
> Min(tmp)
[1] -2.28366
> mean(tmp)
[1] 0.1278625
> Sum(tmp)
[1] 12.78625
> Var(tmp)
[1] 1.111051
>
> rowMeans(tmp)
[1] 0.1278625
> rowSums(tmp)
[1] 12.78625
> rowVars(tmp)
[1] 1.111051
> rowSd(tmp)
[1] 1.054064
> rowMax(tmp)
[1] 2.431375
> rowMin(tmp)
[1] -2.28366
>
> colMeans(tmp)
[1] 0.918048291 -0.005244206 -1.264680627 0.990449446 0.124345754
[6] -0.598876848 1.671579216 -0.748048176 -0.822628340 2.431374546
[11] -0.613208080 0.962096599 0.772342493 -0.291442889 0.465953649
[16] 1.385104638 -0.231559556 0.693557379 0.745749826 1.050113543
[21] -2.283659565 1.465380902 -2.016947023 -0.262519217 -1.037798165
[26] 2.034563204 0.384106439 -0.615098222 -0.779773644 0.336442890
[31] 0.548952613 2.029703139 -0.297936323 1.077127899 -0.423468114
[36] -1.055239831 -1.849616358 0.577028361 -0.739852380 -0.370540628
[41] -0.532585278 0.666706067 0.044475620 0.921856563 -0.058140206
[46] 0.491227215 -0.997730953 -0.398797999 -1.272280748 1.051291710
[51] 1.984380387 0.547330401 -0.507282157 0.977270011 0.380725025
[56] 1.262110662 1.057356595 -0.805573142 0.373694794 -0.036463618
[61] -0.742528728 0.317383130 -0.823413682 0.158088825 -1.522524613
[66] 1.464008986 0.194614156 1.643398789 -0.420904954 -0.989918627
[71] 0.454799591 0.977082305 1.029109212 -2.165938678 -1.276260526
[76] 0.803913006 1.849710338 0.256506385 1.382337544 -0.231555954
[81] 0.066461645 0.746036489 -1.408728768 0.831115567 -1.456976608
[86] -0.980905728 -0.397009564 0.117598555 0.432517505 0.014062187
[91] -1.305810203 1.478218316 1.140112858 0.355430972 0.063451972
[96] 1.443449728 -2.110838312 0.140909634 2.094645163 -0.340850633
> colSums(tmp)
[1] 0.918048291 -0.005244206 -1.264680627 0.990449446 0.124345754
[6] -0.598876848 1.671579216 -0.748048176 -0.822628340 2.431374546
[11] -0.613208080 0.962096599 0.772342493 -0.291442889 0.465953649
[16] 1.385104638 -0.231559556 0.693557379 0.745749826 1.050113543
[21] -2.283659565 1.465380902 -2.016947023 -0.262519217 -1.037798165
[26] 2.034563204 0.384106439 -0.615098222 -0.779773644 0.336442890
[31] 0.548952613 2.029703139 -0.297936323 1.077127899 -0.423468114
[36] -1.055239831 -1.849616358 0.577028361 -0.739852380 -0.370540628
[41] -0.532585278 0.666706067 0.044475620 0.921856563 -0.058140206
[46] 0.491227215 -0.997730953 -0.398797999 -1.272280748 1.051291710
[51] 1.984380387 0.547330401 -0.507282157 0.977270011 0.380725025
[56] 1.262110662 1.057356595 -0.805573142 0.373694794 -0.036463618
[61] -0.742528728 0.317383130 -0.823413682 0.158088825 -1.522524613
[66] 1.464008986 0.194614156 1.643398789 -0.420904954 -0.989918627
[71] 0.454799591 0.977082305 1.029109212 -2.165938678 -1.276260526
[76] 0.803913006 1.849710338 0.256506385 1.382337544 -0.231555954
[81] 0.066461645 0.746036489 -1.408728768 0.831115567 -1.456976608
[86] -0.980905728 -0.397009564 0.117598555 0.432517505 0.014062187
[91] -1.305810203 1.478218316 1.140112858 0.355430972 0.063451972
[96] 1.443449728 -2.110838312 0.140909634 2.094645163 -0.340850633
> colVars(tmp)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> colSd(tmp)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> colMax(tmp)
[1] 0.918048291 -0.005244206 -1.264680627 0.990449446 0.124345754
[6] -0.598876848 1.671579216 -0.748048176 -0.822628340 2.431374546
[11] -0.613208080 0.962096599 0.772342493 -0.291442889 0.465953649
[16] 1.385104638 -0.231559556 0.693557379 0.745749826 1.050113543
[21] -2.283659565 1.465380902 -2.016947023 -0.262519217 -1.037798165
[26] 2.034563204 0.384106439 -0.615098222 -0.779773644 0.336442890
[31] 0.548952613 2.029703139 -0.297936323 1.077127899 -0.423468114
[36] -1.055239831 -1.849616358 0.577028361 -0.739852380 -0.370540628
[41] -0.532585278 0.666706067 0.044475620 0.921856563 -0.058140206
[46] 0.491227215 -0.997730953 -0.398797999 -1.272280748 1.051291710
[51] 1.984380387 0.547330401 -0.507282157 0.977270011 0.380725025
[56] 1.262110662 1.057356595 -0.805573142 0.373694794 -0.036463618
[61] -0.742528728 0.317383130 -0.823413682 0.158088825 -1.522524613
[66] 1.464008986 0.194614156 1.643398789 -0.420904954 -0.989918627
[71] 0.454799591 0.977082305 1.029109212 -2.165938678 -1.276260526
[76] 0.803913006 1.849710338 0.256506385 1.382337544 -0.231555954
[81] 0.066461645 0.746036489 -1.408728768 0.831115567 -1.456976608
[86] -0.980905728 -0.397009564 0.117598555 0.432517505 0.014062187
[91] -1.305810203 1.478218316 1.140112858 0.355430972 0.063451972
[96] 1.443449728 -2.110838312 0.140909634 2.094645163 -0.340850633
> colMin(tmp)
[1] 0.918048291 -0.005244206 -1.264680627 0.990449446 0.124345754
[6] -0.598876848 1.671579216 -0.748048176 -0.822628340 2.431374546
[11] -0.613208080 0.962096599 0.772342493 -0.291442889 0.465953649
[16] 1.385104638 -0.231559556 0.693557379 0.745749826 1.050113543
[21] -2.283659565 1.465380902 -2.016947023 -0.262519217 -1.037798165
[26] 2.034563204 0.384106439 -0.615098222 -0.779773644 0.336442890
[31] 0.548952613 2.029703139 -0.297936323 1.077127899 -0.423468114
[36] -1.055239831 -1.849616358 0.577028361 -0.739852380 -0.370540628
[41] -0.532585278 0.666706067 0.044475620 0.921856563 -0.058140206
[46] 0.491227215 -0.997730953 -0.398797999 -1.272280748 1.051291710
[51] 1.984380387 0.547330401 -0.507282157 0.977270011 0.380725025
[56] 1.262110662 1.057356595 -0.805573142 0.373694794 -0.036463618
[61] -0.742528728 0.317383130 -0.823413682 0.158088825 -1.522524613
[66] 1.464008986 0.194614156 1.643398789 -0.420904954 -0.989918627
[71] 0.454799591 0.977082305 1.029109212 -2.165938678 -1.276260526
[76] 0.803913006 1.849710338 0.256506385 1.382337544 -0.231555954
[81] 0.066461645 0.746036489 -1.408728768 0.831115567 -1.456976608
[86] -0.980905728 -0.397009564 0.117598555 0.432517505 0.014062187
[91] -1.305810203 1.478218316 1.140112858 0.355430972 0.063451972
[96] 1.443449728 -2.110838312 0.140909634 2.094645163 -0.340850633
> colMedians(tmp)
[1] 0.918048291 -0.005244206 -1.264680627 0.990449446 0.124345754
[6] -0.598876848 1.671579216 -0.748048176 -0.822628340 2.431374546
[11] -0.613208080 0.962096599 0.772342493 -0.291442889 0.465953649
[16] 1.385104638 -0.231559556 0.693557379 0.745749826 1.050113543
[21] -2.283659565 1.465380902 -2.016947023 -0.262519217 -1.037798165
[26] 2.034563204 0.384106439 -0.615098222 -0.779773644 0.336442890
[31] 0.548952613 2.029703139 -0.297936323 1.077127899 -0.423468114
[36] -1.055239831 -1.849616358 0.577028361 -0.739852380 -0.370540628
[41] -0.532585278 0.666706067 0.044475620 0.921856563 -0.058140206
[46] 0.491227215 -0.997730953 -0.398797999 -1.272280748 1.051291710
[51] 1.984380387 0.547330401 -0.507282157 0.977270011 0.380725025
[56] 1.262110662 1.057356595 -0.805573142 0.373694794 -0.036463618
[61] -0.742528728 0.317383130 -0.823413682 0.158088825 -1.522524613
[66] 1.464008986 0.194614156 1.643398789 -0.420904954 -0.989918627
[71] 0.454799591 0.977082305 1.029109212 -2.165938678 -1.276260526
[76] 0.803913006 1.849710338 0.256506385 1.382337544 -0.231555954
[81] 0.066461645 0.746036489 -1.408728768 0.831115567 -1.456976608
[86] -0.980905728 -0.397009564 0.117598555 0.432517505 0.014062187
[91] -1.305810203 1.478218316 1.140112858 0.355430972 0.063451972
[96] 1.443449728 -2.110838312 0.140909634 2.094645163 -0.340850633
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] 0.9180483 -0.005244206 -1.264681 0.9904494 0.1243458 -0.5988768 1.671579
[2,] 0.9180483 -0.005244206 -1.264681 0.9904494 0.1243458 -0.5988768 1.671579
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] -0.7480482 -0.8226283 2.431375 -0.6132081 0.9620966 0.7723425 -0.2914429
[2,] -0.7480482 -0.8226283 2.431375 -0.6132081 0.9620966 0.7723425 -0.2914429
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] 0.4659536 1.385105 -0.2315596 0.6935574 0.7457498 1.050114 -2.28366
[2,] 0.4659536 1.385105 -0.2315596 0.6935574 0.7457498 1.050114 -2.28366
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] 1.465381 -2.016947 -0.2625192 -1.037798 2.034563 0.3841064 -0.6150982
[2,] 1.465381 -2.016947 -0.2625192 -1.037798 2.034563 0.3841064 -0.6150982
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] -0.7797736 0.3364429 0.5489526 2.029703 -0.2979363 1.077128 -0.4234681
[2,] -0.7797736 0.3364429 0.5489526 2.029703 -0.2979363 1.077128 -0.4234681
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] -1.05524 -1.849616 0.5770284 -0.7398524 -0.3705406 -0.5325853 0.6667061
[2,] -1.05524 -1.849616 0.5770284 -0.7398524 -0.3705406 -0.5325853 0.6667061
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] 0.04447562 0.9218566 -0.05814021 0.4912272 -0.997731 -0.398798 -1.272281
[2,] 0.04447562 0.9218566 -0.05814021 0.4912272 -0.997731 -0.398798 -1.272281
[,50] [,51] [,52] [,53] [,54] [,55] [,56] [,57]
[1,] 1.051292 1.98438 0.5473304 -0.5072822 0.97727 0.380725 1.262111 1.057357
[2,] 1.051292 1.98438 0.5473304 -0.5072822 0.97727 0.380725 1.262111 1.057357
[,58] [,59] [,60] [,61] [,62] [,63] [,64]
[1,] -0.8055731 0.3736948 -0.03646362 -0.7425287 0.3173831 -0.8234137 0.1580888
[2,] -0.8055731 0.3736948 -0.03646362 -0.7425287 0.3173831 -0.8234137 0.1580888
[,65] [,66] [,67] [,68] [,69] [,70] [,71]
[1,] -1.522525 1.464009 0.1946142 1.643399 -0.420905 -0.9899186 0.4547996
[2,] -1.522525 1.464009 0.1946142 1.643399 -0.420905 -0.9899186 0.4547996
[,72] [,73] [,74] [,75] [,76] [,77] [,78] [,79]
[1,] 0.9770823 1.029109 -2.165939 -1.276261 0.803913 1.84971 0.2565064 1.382338
[2,] 0.9770823 1.029109 -2.165939 -1.276261 0.803913 1.84971 0.2565064 1.382338
[,80] [,81] [,82] [,83] [,84] [,85] [,86]
[1,] -0.231556 0.06646165 0.7460365 -1.408729 0.8311156 -1.456977 -0.9809057
[2,] -0.231556 0.06646165 0.7460365 -1.408729 0.8311156 -1.456977 -0.9809057
[,87] [,88] [,89] [,90] [,91] [,92] [,93]
[1,] -0.3970096 0.1175986 0.4325175 0.01406219 -1.30581 1.478218 1.140113
[2,] -0.3970096 0.1175986 0.4325175 0.01406219 -1.30581 1.478218 1.140113
[,94] [,95] [,96] [,97] [,98] [,99] [,100]
[1,] 0.355431 0.06345197 1.44345 -2.110838 0.1409096 2.094645 -0.3408506
[2,] 0.355431 0.06345197 1.44345 -2.110838 0.1409096 2.094645 -0.3408506
>
>
> Max(tmp2)
[1] 3.160195
> Min(tmp2)
[1] -1.946156
> mean(tmp2)
[1] 0.06928395
> Sum(tmp2)
[1] 6.928395
> Var(tmp2)
[1] 1.052556
>
> rowMeans(tmp2)
[1] -1.946156156 1.391927442 1.259158894 0.485754795 -0.658825018
[6] 0.236771088 0.009075148 0.390670771 -0.385187546 -0.354006990
[11] 2.078266200 -1.226930432 -0.069628484 -1.578069459 1.460945257
[16] -1.367950496 0.051919988 -1.137147200 -1.843350052 -0.839997213
[21] 1.304022812 0.271191230 0.129357500 0.070733970 -0.172191234
[26] -1.002310651 0.641708481 0.202961112 -0.377207992 0.031560576
[31] 0.513845268 3.160195216 1.437226490 -1.220273245 -0.732547055
[36] -1.630597903 -0.501513514 1.702837904 1.115759964 0.668317415
[41] 0.950109757 -0.149574860 1.890466826 1.063831373 -0.363845027
[46] -0.531060540 -0.925966343 -0.087407652 0.596472138 0.080487283
[51] -1.049944002 0.998728341 -0.098135379 0.161804063 0.309329232
[56] 0.299784559 -1.268975983 -0.796516589 -0.163724119 -0.534913260
[61] 0.491430665 -0.841426958 0.330588355 -0.766660654 -0.120979449
[66] 0.739035568 -0.874271089 -0.613109377 -0.435765706 1.705099576
[71] 0.542235579 1.146855368 -1.463488665 0.338864058 -0.184676779
[76] 2.816912343 1.875333534 1.004405028 0.841926542 -1.443157060
[81] -0.506889832 -0.522641302 0.567113217 -1.213090760 0.597316159
[86] 0.582837578 0.355701307 -1.647491041 -0.030010567 -1.705288582
[91] 1.459333162 0.994466510 0.291208181 1.436633136 -0.510405522
[96] 0.045923359 0.125361265 0.007675247 -0.949642591 0.509868185
> rowSums(tmp2)
[1] -1.946156156 1.391927442 1.259158894 0.485754795 -0.658825018
[6] 0.236771088 0.009075148 0.390670771 -0.385187546 -0.354006990
[11] 2.078266200 -1.226930432 -0.069628484 -1.578069459 1.460945257
[16] -1.367950496 0.051919988 -1.137147200 -1.843350052 -0.839997213
[21] 1.304022812 0.271191230 0.129357500 0.070733970 -0.172191234
[26] -1.002310651 0.641708481 0.202961112 -0.377207992 0.031560576
[31] 0.513845268 3.160195216 1.437226490 -1.220273245 -0.732547055
[36] -1.630597903 -0.501513514 1.702837904 1.115759964 0.668317415
[41] 0.950109757 -0.149574860 1.890466826 1.063831373 -0.363845027
[46] -0.531060540 -0.925966343 -0.087407652 0.596472138 0.080487283
[51] -1.049944002 0.998728341 -0.098135379 0.161804063 0.309329232
[56] 0.299784559 -1.268975983 -0.796516589 -0.163724119 -0.534913260
[61] 0.491430665 -0.841426958 0.330588355 -0.766660654 -0.120979449
[66] 0.739035568 -0.874271089 -0.613109377 -0.435765706 1.705099576
[71] 0.542235579 1.146855368 -1.463488665 0.338864058 -0.184676779
[76] 2.816912343 1.875333534 1.004405028 0.841926542 -1.443157060
[81] -0.506889832 -0.522641302 0.567113217 -1.213090760 0.597316159
[86] 0.582837578 0.355701307 -1.647491041 -0.030010567 -1.705288582
[91] 1.459333162 0.994466510 0.291208181 1.436633136 -0.510405522
[96] 0.045923359 0.125361265 0.007675247 -0.949642591 0.509868185
> rowVars(tmp2)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> rowSd(tmp2)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> rowMax(tmp2)
[1] -1.946156156 1.391927442 1.259158894 0.485754795 -0.658825018
[6] 0.236771088 0.009075148 0.390670771 -0.385187546 -0.354006990
[11] 2.078266200 -1.226930432 -0.069628484 -1.578069459 1.460945257
[16] -1.367950496 0.051919988 -1.137147200 -1.843350052 -0.839997213
[21] 1.304022812 0.271191230 0.129357500 0.070733970 -0.172191234
[26] -1.002310651 0.641708481 0.202961112 -0.377207992 0.031560576
[31] 0.513845268 3.160195216 1.437226490 -1.220273245 -0.732547055
[36] -1.630597903 -0.501513514 1.702837904 1.115759964 0.668317415
[41] 0.950109757 -0.149574860 1.890466826 1.063831373 -0.363845027
[46] -0.531060540 -0.925966343 -0.087407652 0.596472138 0.080487283
[51] -1.049944002 0.998728341 -0.098135379 0.161804063 0.309329232
[56] 0.299784559 -1.268975983 -0.796516589 -0.163724119 -0.534913260
[61] 0.491430665 -0.841426958 0.330588355 -0.766660654 -0.120979449
[66] 0.739035568 -0.874271089 -0.613109377 -0.435765706 1.705099576
[71] 0.542235579 1.146855368 -1.463488665 0.338864058 -0.184676779
[76] 2.816912343 1.875333534 1.004405028 0.841926542 -1.443157060
[81] -0.506889832 -0.522641302 0.567113217 -1.213090760 0.597316159
[86] 0.582837578 0.355701307 -1.647491041 -0.030010567 -1.705288582
[91] 1.459333162 0.994466510 0.291208181 1.436633136 -0.510405522
[96] 0.045923359 0.125361265 0.007675247 -0.949642591 0.509868185
> rowMin(tmp2)
[1] -1.946156156 1.391927442 1.259158894 0.485754795 -0.658825018
[6] 0.236771088 0.009075148 0.390670771 -0.385187546 -0.354006990
[11] 2.078266200 -1.226930432 -0.069628484 -1.578069459 1.460945257
[16] -1.367950496 0.051919988 -1.137147200 -1.843350052 -0.839997213
[21] 1.304022812 0.271191230 0.129357500 0.070733970 -0.172191234
[26] -1.002310651 0.641708481 0.202961112 -0.377207992 0.031560576
[31] 0.513845268 3.160195216 1.437226490 -1.220273245 -0.732547055
[36] -1.630597903 -0.501513514 1.702837904 1.115759964 0.668317415
[41] 0.950109757 -0.149574860 1.890466826 1.063831373 -0.363845027
[46] -0.531060540 -0.925966343 -0.087407652 0.596472138 0.080487283
[51] -1.049944002 0.998728341 -0.098135379 0.161804063 0.309329232
[56] 0.299784559 -1.268975983 -0.796516589 -0.163724119 -0.534913260
[61] 0.491430665 -0.841426958 0.330588355 -0.766660654 -0.120979449
[66] 0.739035568 -0.874271089 -0.613109377 -0.435765706 1.705099576
[71] 0.542235579 1.146855368 -1.463488665 0.338864058 -0.184676779
[76] 2.816912343 1.875333534 1.004405028 0.841926542 -1.443157060
[81] -0.506889832 -0.522641302 0.567113217 -1.213090760 0.597316159
[86] 0.582837578 0.355701307 -1.647491041 -0.030010567 -1.705288582
[91] 1.459333162 0.994466510 0.291208181 1.436633136 -0.510405522
[96] 0.045923359 0.125361265 0.007675247 -0.949642591 0.509868185
>
> colMeans(tmp2)
[1] 0.06928395
> colSums(tmp2)
[1] 6.928395
> colVars(tmp2)
[1] 1.052556
> colSd(tmp2)
[1] 1.025942
> colMax(tmp2)
[1] 3.160195
> colMin(tmp2)
[1] -1.946156
> colMedians(tmp2)
[1] 0.04892167
> colRanges(tmp2)
[,1]
[1,] -1.946156
[2,] 3.160195
>
> dataset1 <- matrix(dataset1,1,100)
>
> agree.checks(tmp,dataset1)
>
> dataset2 <- matrix(dataset2,100,1)
> agree.checks(tmp2,dataset2)
>
>
> tmp <- createBufferedMatrix(10,10)
>
> tmp[1:10,1:10] <- rnorm(100)
> colApply(tmp,sum)
[1] 1.93084357 2.48553881 -3.49400756 -2.68415235 5.39229448 0.77195039
[7] -7.25237020 -0.06839657 2.39511019 0.07111087
> colApply(tmp,quantile)[,1]
[,1]
[1,] -0.96329178
[2,] -0.14796674
[3,] 0.05393971
[4,] 0.74311185
[5,] 1.51420128
>
> rowApply(tmp,sum)
[1] 3.7819817 -0.1099937 0.6352221 3.1839220 -0.8548876 -2.6136593
[7] 4.1103111 -4.2728514 -0.9558064 -3.3563169
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 7 5 5 9 8 6 9 4 5 3
[2,] 3 10 10 6 3 5 1 3 4 9
[3,] 5 6 6 5 4 7 6 6 2 1
[4,] 9 1 3 3 7 8 2 1 6 5
[5,] 10 4 9 4 10 4 8 8 7 7
[6,] 4 7 2 7 1 10 7 2 9 10
[7,] 1 9 7 2 9 1 3 5 1 4
[8,] 6 3 4 10 2 3 4 7 3 6
[9,] 2 8 8 1 6 2 10 9 10 8
[10,] 8 2 1 8 5 9 5 10 8 2
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] -1.618363989 2.300160788 1.371996002 1.427450963 0.820852570
[6] 1.124922365 4.175207335 -0.687696767 0.064983349 -5.214241685
[11] 0.003526699 0.965120568 -4.166392041 -1.605534570 -0.624437577
[16] -0.998984572 1.082082565 0.433841169 3.580371429 0.536280774
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.6572911
[2,] -1.2408122
[3,] 0.2723648
[4,] 0.3629013
[5,] 0.6444733
>
> rowApply(tmp,sum)
[1] 0.3917797 0.3859784 -4.7218204 3.2834234 3.6317843
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 13 2 3 13 15
[2,] 14 11 6 19 16
[3,] 18 12 8 16 5
[4,] 5 4 16 15 17
[5,] 8 7 14 4 19
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 0.2723648 0.3495435 1.0012866 -0.3029965 0.08967606 1.0773515
[2,] -1.2408122 0.4031350 0.4251505 -0.7147756 -0.37049990 0.4947898
[3,] -1.6572911 -0.9891587 -0.6501461 0.8676407 0.43494122 -0.1713153
[4,] 0.3629013 1.8597469 1.1683474 0.8517586 -0.65672084 -0.7966731
[5,] 0.6444733 0.6768941 -0.5726425 0.7258238 1.32345603 0.5207695
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] 1.10900111 -2.7145622 0.1456347 0.1904353 0.7150241 -0.1774183
[2,] 1.24641684 1.3873477 0.5928911 -2.3218145 0.3451602 -0.1428298
[3,] 0.09056989 1.2639132 -0.6097648 -1.0449692 0.1929003 1.0380281
[4,] 1.55218403 -0.3348035 0.6262382 -0.6340897 -0.5925346 -0.1881769
[5,] 0.17703547 -0.2895920 -0.6900158 -1.4038036 -0.6570232 0.4355175
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] 0.1415644 -1.5140706 -0.8867673 -0.2736461 0.7561149 -0.5112233
[2,] 0.5442836 -0.5695051 0.6049842 -1.1633468 0.3720290 -0.6722176
[3,] -2.4409316 -0.6650193 -1.8119578 1.0727456 0.8848922 -0.3108185
[4,] -2.2684259 -0.1795694 2.6181897 -0.2864472 -1.2131127 1.3167913
[5,] -0.1428826 1.3226298 -1.1488863 -0.3482901 0.2821591 0.6113091
[,19] [,20]
[1,] 0.7041818 0.2202851
[2,] 0.6150849 0.5505073
[3,] 0.8421796 -1.0582589
[4,] -0.1190184 0.1968382
[5,] 1.5379435 0.6269091
>
>
> is.BufferedMatrix(tmp)
[1] TRUE
>
> as.BufferedMatrix(as.matrix(tmp))
BufferedMatrix object
Matrix size: 5 20
Buffer size: 1 1
Directory: F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.8 Kilobytes.
Disk usage : 800 bytes.
>
>
>
> subBufferedMatrix(tmp,1:5,1:5)
BufferedMatrix object
Matrix size: 5 5
Buffer size: 1 1
Directory: F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 625 bytes.
Disk usage : 200 bytes.
> subBufferedMatrix(tmp,,5:8)
BufferedMatrix object
Matrix size: 5 4
Buffer size: 1 1
Directory: F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 543 bytes.
Disk usage : 160 bytes.
> subBufferedMatrix(tmp,1:3,)
BufferedMatrix object
Matrix size: 3 20
Buffer size: 1 1
Directory: F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.8 Kilobytes.
Disk usage : 480 bytes.
>
>
> rm(tmp)
>
>
> ###
> ### Testing colnames and rownames
> ###
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
>
>
> colnames(tmp)
NULL
> rownames(tmp)
NULL
>
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
> colnames(tmp)
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
> rownames(tmp)
[1] "row1" "row2" "row3" "row4" "row5"
>
>
> tmp["row1",]
col1 col2 col3 col4 col5 col6 col7
row1 0.145366 0.6763614 0.2152627 1.268439 -0.6597425 0.6355925 -2.120843
col8 col9 col10 col11 col12 col13 col14
row1 -0.5056222 -1.66994 -1.981056 -1.150869 -0.01821097 -0.3486545 -2.55979
col15 col16 col17 col18 col19 col20
row1 -0.7063093 -2.265934 -0.3042022 -1.356521 0.5454391 -0.2547687
> tmp[,"col10"]
col10
row1 -1.98105579
row2 -0.01285233
row3 0.80658728
row4 1.10001813
row5 0.59052941
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6
row1 0.1453660 0.6763614 0.2152627 1.26843939 -0.6597425 0.6355925
row5 -0.7648496 0.9483757 -1.8501798 -0.04029684 -0.7616815 -0.3335746
col7 col8 col9 col10 col11 col12
row1 -2.120843 -0.5056222 -1.6699396 -1.9810558 -1.1508690 -0.01821097
row5 -0.245996 0.5061372 -0.1175964 0.5905294 -0.8624632 0.95870994
col13 col14 col15 col16 col17 col18 col19
row1 -0.3486545 -2.559790 -0.7063093 -2.2659335 -0.3042022 -1.356521 0.5454391
row5 1.6271362 1.193112 -0.5887328 0.8313982 1.1585171 1.541471 1.5544882
col20
row1 -0.2547687
row5 -1.6578166
> tmp[,c("col6","col20")]
col6 col20
row1 0.6355925 -0.2547687
row2 -0.5784424 -0.4111974
row3 -1.4923761 -0.3646743
row4 0.3897216 1.9939181
row5 -0.3335746 -1.6578166
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 0.6355925 -0.2547687
row5 -0.3335746 -1.6578166
>
>
>
>
> tmp["row1",] <- rnorm(20,mean=10)
> tmp[,"col10"] <- rnorm(5,mean=30)
> tmp[c("row1","row5"),] <- rnorm(40,mean=50)
> tmp[,c("col6","col20")] <- rnorm(10,mean=75)
> tmp[c("row1","row5"),c("col6","col20")] <- rnorm(4,mean=105)
>
> tmp["row1",]
col1 col2 col3 col4 col5 col6 col7 col8
row1 50.42216 49.84952 51.33606 51.40211 50.69643 103.5014 48.61299 50.50808
col9 col10 col11 col12 col13 col14 col15 col16
row1 50.73474 49.97248 49.4614 50.12623 48.1796 50.19092 50.8014 51.65537
col17 col18 col19 col20
row1 50.20322 49.79283 51.26712 104.9258
> tmp[,"col10"]
col10
row1 49.97248
row2 28.38205
row3 30.40901
row4 32.15102
row5 50.55521
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 50.42216 49.84952 51.33606 51.40211 50.69643 103.5014 48.61299 50.50808
row5 51.10417 50.34787 52.12237 48.25894 49.24972 106.2857 51.25979 49.26351
col9 col10 col11 col12 col13 col14 col15 col16
row1 50.73474 49.97248 49.46140 50.12623 48.1796 50.19092 50.80140 51.65537
row5 48.78587 50.55521 49.13624 51.17550 49.1438 49.39463 50.54454 49.36557
col17 col18 col19 col20
row1 50.20322 49.79283 51.26712 104.9258
row5 49.27848 50.89474 50.05032 103.9426
> tmp[,c("col6","col20")]
col6 col20
row1 103.50145 104.92582
row2 74.64838 75.12592
row3 76.14541 75.20265
row4 73.82457 73.69745
row5 106.28574 103.94260
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 103.5014 104.9258
row5 106.2857 103.9426
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 103.5014 104.9258
row5 106.2857 103.9426
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] 0.58768907
[2,] -0.24227057
[3,] -0.04286161
[4,] 1.37403514
[5,] -1.69408899
> tmp[,c("col17","col7")]
col17 col7
[1,] 1.9978858 -2.0614408
[2,] 1.0842517 0.3257688
[3,] -0.4080783 -0.6593050
[4,] 0.1150028 -0.8133824
[5,] -1.1365252 -0.6602829
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] -0.08198092 -0.5814605
[2,] 0.09270301 0.4465646
[3,] 2.11308760 0.5921889
[4,] -1.68326494 0.1769130
[5,] -0.65038070 0.6892237
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] -0.08198092
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] -0.08198092
[2,] 0.09270301
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
>
>
>
> subBufferedMatrix(tmp,c("row3","row1"),)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6]
row3 0.02112387 -0.8297453 1.2939416 -1.4122096 0.4793997 -0.5307283
row1 0.10820556 0.2099913 -0.2736278 0.1894607 0.9987710 -0.2667696
[,7] [,8] [,9] [,10] [,11] [,12]
row3 0.8554466 2.855675 1.322328 1.2526667 1.0578177 0.418795487
row1 -2.4176700 -1.142707 -1.048634 -0.1096922 -0.4839359 0.004188126
[,13] [,14] [,15] [,16] [,17] [,18] [,19]
row3 0.4254559 0.8922340 -1.5566383 1.609051 0.9985107 1.012354 1.90756381
row1 -0.3191350 -0.2729061 -0.3685037 1.576807 -2.0291798 -1.668908 -0.03602221
[,20]
row3 -0.1276938
row1 -0.6824479
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 -0.9634559 -1.46776 -0.09624913 -0.4176308 0.3653287 -0.1111401 -0.8134864
[,8] [,9] [,10]
row2 -0.2730029 -0.3903885 0.2642643
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 -0.1752693 0.8290126 0.708299 -0.6335955 0.9002308 0.1497179 1.487922
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 1.686969 -1.103056 -0.04350857 0.1193001 0.5906333 -0.5683044 0.1127107
[,15] [,16] [,17] [,18] [,19] [,20]
row5 1.763402 1.754807 0.2759802 -0.4612566 -0.3391462 -0.00628025
>
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
> colnames(tmp)
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
> rownames(tmp)
[1] "row1" "row2" "row3" "row4" "row5"
>
>
> colnames(tmp) <- NULL
> rownames(tmp) <- NULL
>
> colnames(tmp)
NULL
> rownames(tmp)
NULL
>
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
> dimnames(tmp)
[[1]]
[1] "row1" "row2" "row3" "row4" "row5"
[[2]]
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
>
> dimnames(tmp) <- NULL
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> dimnames(tmp)
[[1]]
NULL
[[2]]
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
>
>
> dimnames(tmp) <- NULL
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
> dimnames(tmp)
[[1]]
[1] "row1" "row2" "row3" "row4" "row5"
[[2]]
NULL
>
> dimnames(tmp) <- list(NULL,c(colnames(tmp,do.NULL=FALSE)))
> dimnames(tmp)
[[1]]
NULL
[[2]]
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
>
>
>
> ###
> ### Testing logical indexing
> ###
> ###
>
> tmp <- createBufferedMatrix(230,15)
> tmp[1:230,1:15] <- rnorm(230*15)
> x <-tmp[1:230,1:15]
>
> for (rep in 1:10){
+ which.cols <- sample(c(TRUE,FALSE),15,replace=T)
+ which.rows <- sample(c(TRUE,FALSE),230,replace=T)
+
+ if (!all(tmp[which.rows,which.cols] == x[which.rows,which.cols])){
+ stop("No agreement when logical indexing\n")
+ }
+
+ if (!all(subBufferedMatrix(tmp,,which.cols)[,1:sum(which.cols)] == x[,which.cols])){
+ stop("No agreement when logical indexing in subBufferedMatrix cols\n")
+ }
+ if (!all(subBufferedMatrix(tmp,which.rows,)[1:sum(which.rows),] == x[which.rows,])){
+ stop("No agreement when logical indexing in subBufferedMatrix rows\n")
+ }
+
+
+ if (!all(subBufferedMatrix(tmp,which.rows,which.cols)[1:sum(which.rows),1:sum(which.cols)]== x[which.rows,which.cols])){
+ stop("No agreement when logical indexing in subBufferedMatrix rows and columns\n")
+ }
+ }
>
>
> ##
> ## Test the ReadOnlyMode
> ##
>
> ReadOnlyMode(tmp)
<pointer: 0x000002cf124ff110>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM374041f95485"
[2] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM3740f2a7e92"
[3] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM37402fbf45b6"
[4] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM374050493059"
[5] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM3740213e2a02"
[6] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM3740114a5ae9"
[7] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM3740331a310c"
[8] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM374072914f22"
[9] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM37401c8377d7"
[10] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM3740156935"
[11] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM37403eb66a35"
[12] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM374047a610b7"
[13] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM37404dc65882"
[14] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM3740128935f5"
[15] "F:/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests\\BM3740769c1591"
>
>
> ### testing coercion functions
> ###
>
> tmp <- as(tmp,"matrix")
> tmp <- as(tmp,"BufferedMatrix")
>
>
>
> ### testing whether can move storage from one location to another
>
> MoveStorageDirectory(tmp,"NewDirectory",full.path=FALSE)
<pointer: 0x000002cf151ffb30>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x000002cf151ffb30>
Warning message:
In dir.create(new.directory) :
'F:\biocbuild\bbs-3.20-bioc\meat\BufferedMatrix.Rcheck\tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x000002cf151ffb30>
> rowMedians(tmp)
[1] 0.336069331 -0.290181076 -0.104930498 -0.278894171 -0.275163227
[6] 0.523896256 0.094572632 0.129929894 -0.003445909 0.298567434
[11] 0.258672662 0.147740152 -0.034066125 0.368099036 -0.484769502
[16] -0.176331089 0.384621370 -0.091195136 -0.097499657 0.142052953
[21] -0.667582238 -0.717127796 -0.038415039 0.661103127 -0.010507586
[26] -0.060564835 0.035313532 -0.696587650 0.387513067 -0.269368059
[31] 0.310513440 -0.301583378 0.040441920 -0.230810630 -0.480401525
[36] 0.142696304 -0.556584262 0.162128712 0.488304734 -0.394986553
[41] 0.036116594 0.090741409 0.130950175 0.308513744 -0.031141549
[46] 0.452432345 0.102849527 -0.117812705 0.359736565 -0.311428845
[51] 0.326388545 -0.413631997 0.249640695 0.108135677 -0.302541137
[56] 0.549277461 -0.078216582 -0.510134943 -0.413791627 0.265437166
[61] -0.521063268 0.270700892 -0.014165881 0.244954923 -0.065041417
[66] -0.246983398 0.381163335 0.134070334 0.521394424 0.013770342
[71] 0.068225000 -0.104774938 -0.181036202 -0.414091349 0.262984098
[76] 0.350793708 0.123069038 -0.337178569 -0.140945974 -0.016523662
[81] -0.235230975 0.259072115 -0.544152173 -0.105074415 -0.187030490
[86] 0.224341478 -0.444185349 0.198083261 -0.570774898 0.281794405
[91] 0.397015573 -0.456167054 -0.885494263 0.064912137 -0.835599217
[96] -0.210205416 0.096293330 -0.075867715 0.104749103 -0.881188417
[101] 0.343029577 0.202099692 -0.508289593 -0.307656346 0.565584491
[106] -0.199678618 0.431110828 0.120992407 -0.082389928 -0.191457725
[111] 0.137023809 -0.231527039 0.557845558 -0.110864478 0.124108584
[116] 0.303274568 -0.258857338 0.023723783 -0.205006961 0.023834034
[121] -0.130817196 0.523035870 0.048895610 0.219302896 -0.630547242
[126] -0.407479731 -0.315364883 -0.182471094 0.050573371 -0.229847379
[131] 0.029136955 0.015670887 -0.147084532 -0.290271413 0.641568134
[136] -0.352030592 -0.008070950 -0.290683211 -0.240942064 0.467731284
[141] -0.111005459 0.082521623 -0.266859638 -0.385492486 -0.033595057
[146] -0.655448641 -0.001433192 -0.087878340 0.236103611 0.343450395
[151] 0.130962698 0.454556997 0.117630815 -0.244065813 -0.687117218
[156] -0.015214338 -0.636352748 0.088982426 -0.710548657 -0.267445887
[161] -0.332806077 -0.181847059 0.183821682 0.191154494 -0.403151693
[166] -0.278738092 -0.219477740 0.278182277 -0.123611258 -0.750469816
[171] -0.352176089 0.138765097 0.235101346 -0.275745799 -0.150513034
[176] -0.307932809 -0.300321937 -0.071778056 -0.403753028 0.463874856
[181] -0.122694398 0.166373146 -0.269931079 -0.472535763 -0.046958065
[186] 0.015234955 -0.328860415 0.166317168 -0.353726126 0.568481225
[191] 0.018444307 -0.020297463 -0.317531190 -0.307595727 0.464032959
[196] -0.090110346 0.073361635 -0.472396790 -0.072823775 -0.225829865
[201] -0.157511061 0.152006712 0.103265893 -0.158405627 0.012058509
[206] -0.666016470 0.152235668 0.242242648 0.188955369 -0.451118664
[211] -0.130371476 0.106565696 -0.365992956 -0.242511151 -0.178594269
[216] 0.006595958 -0.173402150 -0.110303421 0.013738533 -0.583587349
[221] -0.129694120 -0.109389387 0.007071794 0.189569072 0.453597803
[226] 0.200338909 0.285615967 0.351364492 -0.098877648 -0.125741058
>
> proc.time()
user system elapsed
4.37 26.01 122.17
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths());
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
>
> prefix <- "dbmtest"
> directory <- getwd()
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_Test_C",P)
RBufferedMatrix
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x000002cb0b0f9710>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x000002cb0b0f9710>
> .Call("R_bm_Test_C",P)
RBufferedMatrix
Checking dimensions
Rows: 5
Cols: 10
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x000002cb0b0f9710>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 10
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 1.000000 2.000000 3.000000 4.000000 0.000000 0.000000 0.000000 0.000000 0.000000
1.000000 2.000000 3.000000 4.000000 5.000000 0.000000 0.000000 0.000000 0.000000 0.000000
2.000000 3.000000 4.000000 5.000000 6.000000 0.000000 0.000000 0.000000 0.000000 0.000000
3.000000 4.000000 5.000000 6.000000 7.000000 0.000000 0.000000 0.000000 0.000000 0.000000
4.000000 5.000000 6.000000 7.000000 8.000000 0.000000 0.000000 0.000000 0.000000 0.000000
<pointer: 0x000002cb0b0f9710>
> rm(P)
>
> #P <- .Call("R_bm_Destroy",P)
> #.Call("R_bm_Destroy",P)
> #.Call("R_bm_Test_C",P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,5)
[1] TRUE
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 0
Buffer Rows: 1
Buffer Cols: 1
Printing Values
<pointer: 0x000002cb0b0f98f0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x000002cb0b0f98f0>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 1
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000
0.000000
0.000000
0.000000
0.000000
<pointer: 0x000002cb0b0f98f0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x000002cb0b0f98f0>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x000002cb0b0f98f0>
> rm(P)
>
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,5)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x000002cb0b0f92f0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x000002cb0b0f92f0>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x000002cb0b0f92f0>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x000002cb0b0f92f0>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 5
Buffer Cols: 5
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x000002cb0b0f92f0>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x000002cb0b0f92f0>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 5
Buffer Cols: 5
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x000002cb0b0f92f0>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x000002cb0b0f92f0>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 5
Buffer Cols: 5
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x000002cb0b0f92f0>
> rm(P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x000002cb0b0f9470>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x000002cb0b0f9470>
> .Call("R_bm_AddColumn",P)
<pointer: 0x000002cb0b0f9470>
> .Call("R_bm_AddColumn",P)
<pointer: 0x000002cb0b0f9470>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile1068142b3cd3" "BufferedMatrixFile10687ed52dc2"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile1068142b3cd3" "BufferedMatrixFile10687ed52dc2"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x000002cb0b0f9890>
> .Call("R_bm_AddColumn",P)
<pointer: 0x000002cb0b0f9890>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x000002cb0b0f9890>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x000002cb0b0f9890>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x000002cb0b0f9890>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x000002cb0b0f9890>
> .Call("R_bm_isRowMode",P)
[1] FALSE
> rm(P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x000002cb0b0f9050>
> .Call("R_bm_AddColumn",P)
<pointer: 0x000002cb0b0f9050>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x000002cb0b0f9050>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x000002cb0b0f9050>
> rm(P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_Test_C",P)
RBufferedMatrix
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x000002cb0b0f9a70>
> .Call("R_bm_getValue",P,3,3)
[1] 6
>
> .Call("R_bm_getValue",P,100000,10000)
[1] NA
> .Call("R_bm_setValue",P,3,3,12345.0)
[1] TRUE
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 12345.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x000002cb0b0f9a70>
> rm(P)
>
> proc.time()
user system elapsed
0.29 0.17 0.96
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
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Platform: x86_64-w64-mingw32/x64
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You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
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'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths());
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
>
> Temp <- createBufferedMatrix(100)
> dim(Temp)
[1] 100 0
> buffer.dim(Temp)
[1] 1 1
>
>
> proc.time()
user system elapsed
0.28 0.09 0.34