Ben Bolstad
| Snapshot Date: 2024-12-30 13:00 -0500 (Mon, 30 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/BufferedMatrix |
| git_branch: RELEASE_3_20 |
| git_last_commit: 32b6f6a |
| git_last_commit_date: 2024-10-29 09:27:20 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-01-02 12:05 -0500 (Thu, 02 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| 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 251/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BufferedMatrix 1.70.0 (landing page) Ben Bolstad
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | 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: 1.70.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BufferedMatrix_1.70.0.tar.gz |
| StartedAt: 2024-12-31 00:45:14 -0500 (Tue, 31 Dec 2024) |
| EndedAt: 2024-12-31 00:46:35 -0500 (Tue, 31 Dec 2024) |
| EllapsedTime: 80.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: BufferedMatrix.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BufferedMatrix_1.70.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BufferedMatrix/DESCRIPTION’ ... OK
* this is package ‘BufferedMatrix’ version ‘1.70.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘BufferedMatrix’ can be installed ... WARNING
Found the following significant warnings:
doubleBufferedMatrix.c:1580:7: warning: logical not is only applied to the left hand side of this bitwise operator [-Wlogical-not-parentheses]
See ‘/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 is not available
* 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: 1 WARNING, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/00check.log’
for details.
BufferedMatrix.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BufferedMatrix
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘BufferedMatrix’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RBufferedMatrix.c -o RBufferedMatrix.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c doubleBufferedMatrix.c -o doubleBufferedMatrix.o
doubleBufferedMatrix.c:1580:7: warning: logical not is only applied to the left hand side of this bitwise operator [-Wlogical-not-parentheses]
if (!(Matrix->readonly) & setting){
^ ~
doubleBufferedMatrix.c:1580:7: note: add parentheses after the '!' to evaluate the bitwise operator first
if (!(Matrix->readonly) & setting){
^
( )
doubleBufferedMatrix.c:1580:7: note: add parentheses around left hand side expression to silence this warning
if (!(Matrix->readonly) & setting){
^
( )
doubleBufferedMatrix.c:3327:12: warning: unused function 'sort_double' [-Wunused-function]
static int sort_double(const double *a1,const double *a2){
^
2 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c doubleBufferedMatrix_C_tests.c -o doubleBufferedMatrix_C_tests.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c init_package.c -o init_package.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o BufferedMatrix.so RBufferedMatrix.o doubleBufferedMatrix.o doubleBufferedMatrix_C_tests.o init_package.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-BufferedMatrix/00new/BufferedMatrix/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** 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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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
0.603 0.211 0.834
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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] "/Users/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) limit (Mb) max used (Mb)
Ncells 474188 25.4 1035498 55.4 NA 638648 34.2
Vcells 877698 6.7 8388608 64.0 65536 2071806 15.9
>
>
>
>
> ##
> ## 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] "Tue Dec 31 00:45:51 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] "Tue Dec 31 00:45:52 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: 0x600001604000>
>
>
>
> 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] "Tue Dec 31 00:45:58 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] "Tue Dec 31 00:46:01 2024"
>
> ColMode(tmp2)
<pointer: 0x600001604000>
>
>
>
> ### 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,] 101.1477570 -0.6720017 -0.06039546 -0.4485392
[2,] 0.5825327 -1.1632244 -0.41717929 -1.0238724
[3,] 1.1470315 1.2471917 0.61794698 0.4271792
[4,] -1.5835776 0.1886845 -0.01812806 -1.6489069
> ewApply(tmp5,abs)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /Users/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,] 101.1477570 0.6720017 0.06039546 0.4485392
[2,] 0.5825327 1.1632244 0.41717929 1.0238724
[3,] 1.1470315 1.2471917 0.61794698 0.4271792
[4,] 1.5835776 0.1886845 0.01812806 1.6489069
> ewApply(tmp5,sqrt)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /Users/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,] 10.0572241 0.8197571 0.2457549 0.6697307
[2,] 0.7632383 1.0785288 0.6458942 1.0118658
[3,] 1.0709956 1.1167774 0.7860960 0.6535894
[4,] 1.2584028 0.4343783 0.1346405 1.2840977
>
> 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: /Users/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,] 226.72000 33.86957 27.51794 32.14585
[2,] 33.21492 36.94851 31.87612 36.14253
[3,] 36.85699 37.41497 33.47891 31.96307
[4,] 39.16761 29.53247 26.36453 39.48988
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x600001624480>
> exp(tmp5)
<pointer: 0x600001624480>
> log(tmp5,2)
<pointer: 0x600001624480>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 471.888
> Min(tmp5)
[1] 52.93269
> mean(tmp5)
[1] 73.50329
> Sum(tmp5)
[1] 14700.66
> Var(tmp5)
[1] 877.4734
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 88.43521 72.67335 75.52728 69.20182 69.72536 70.59007 72.59682 73.55107
[9] 73.06312 69.66875
> rowSums(tmp5)
[1] 1768.704 1453.467 1510.546 1384.036 1394.507 1411.801 1451.936 1471.021
[9] 1461.262 1393.375
> rowVars(tmp5)
[1] 8238.41695 43.60116 63.10485 74.15423 81.55860 53.06237
[7] 95.85426 92.80420 78.75633 69.34888
> rowSd(tmp5)
[1] 90.765726 6.603118 7.943856 8.611285 9.030980 7.284392 9.790519
[8] 9.633494 8.874476 8.327598
> rowMax(tmp5)
[1] 471.88797 82.80699 88.47108 85.77190 92.24189 81.64101 89.06324
[8] 90.84129 94.49507 87.58414
> rowMin(tmp5)
[1] 54.90614 58.47248 63.35070 54.87432 57.02413 56.83312 55.87786 56.24669
[9] 56.33430 52.93269
>
> colMeans(tmp5)
[1] 114.91103 73.97899 69.22263 71.27192 73.39669 67.84105 73.68707
[8] 75.71998 73.51435 71.00823 74.74490 73.69173 69.53766 71.12888
[15] 72.62643 68.37667 69.47641 66.59508 69.34440 69.99160
> colSums(tmp5)
[1] 1149.1103 739.7899 692.2263 712.7192 733.9669 678.4105 736.8707
[8] 757.1998 735.1435 710.0823 747.4490 736.9173 695.3766 711.2888
[15] 726.2643 683.7667 694.7641 665.9508 693.4440 699.9160
> colVars(tmp5)
[1] 15752.85358 58.99130 116.82443 41.67618 32.77550 113.96907
[7] 69.59512 61.27904 87.12523 89.05863 64.78614 73.54395
[13] 42.94654 136.79979 66.77462 87.84352 101.23438 126.14590
[19] 99.93107 38.93964
> colSd(tmp5)
[1] 125.510372 7.680580 10.808535 6.455709 5.724989 10.675630
[7] 8.342369 7.828093 9.334090 9.437088 8.048984 8.575777
[13] 6.553361 11.696144 8.171574 9.372487 10.061530 11.231469
[19] 9.996553 6.240163
> colMax(tmp5)
[1] 471.88797 90.84129 92.24189 82.19302 85.77190 89.06324 82.56907
[8] 87.02651 87.94916 87.58414 88.47108 86.59288 78.96707 94.49507
[15] 85.21942 86.69626 84.42422 92.85615 85.09205 76.95736
> colMin(tmp5)
[1] 69.13249 61.46796 54.87432 62.59414 67.19973 54.90614 55.87786 58.99700
[9] 58.80155 58.47248 63.26806 56.62032 60.27974 55.51844 61.65051 55.16647
[17] 56.83312 52.93269 56.93576 59.94335
>
>
> ### 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] 88.43521 72.67335 75.52728 69.20182 69.72536 70.59007 72.59682 73.55107
[9] NA 69.66875
> rowSums(tmp5)
[1] 1768.704 1453.467 1510.546 1384.036 1394.507 1411.801 1451.936 1471.021
[9] NA 1393.375
> rowVars(tmp5)
[1] 8238.41695 43.60116 63.10485 74.15423 81.55860 53.06237
[7] 95.85426 92.80420 83.11033 69.34888
> rowSd(tmp5)
[1] 90.765726 6.603118 7.943856 8.611285 9.030980 7.284392 9.790519
[8] 9.633494 9.116486 8.327598
> rowMax(tmp5)
[1] 471.88797 82.80699 88.47108 85.77190 92.24189 81.64101 89.06324
[8] 90.84129 NA 87.58414
> rowMin(tmp5)
[1] 54.90614 58.47248 63.35070 54.87432 57.02413 56.83312 55.87786 56.24669
[9] NA 52.93269
>
> colMeans(tmp5)
[1] 114.91103 73.97899 69.22263 71.27192 73.39669 67.84105 73.68707
[8] 75.71998 73.51435 NA 74.74490 73.69173 69.53766 71.12888
[15] 72.62643 68.37667 69.47641 66.59508 69.34440 69.99160
> colSums(tmp5)
[1] 1149.1103 739.7899 692.2263 712.7192 733.9669 678.4105 736.8707
[8] 757.1998 735.1435 NA 747.4490 736.9173 695.3766 711.2888
[15] 726.2643 683.7667 694.7641 665.9508 693.4440 699.9160
> colVars(tmp5)
[1] 15752.85358 58.99130 116.82443 41.67618 32.77550 113.96907
[7] 69.59512 61.27904 87.12523 NA 64.78614 73.54395
[13] 42.94654 136.79979 66.77462 87.84352 101.23438 126.14590
[19] 99.93107 38.93964
> colSd(tmp5)
[1] 125.510372 7.680580 10.808535 6.455709 5.724989 10.675630
[7] 8.342369 7.828093 9.334090 NA 8.048984 8.575777
[13] 6.553361 11.696144 8.171574 9.372487 10.061530 11.231469
[19] 9.996553 6.240163
> colMax(tmp5)
[1] 471.88797 90.84129 92.24189 82.19302 85.77190 89.06324 82.56907
[8] 87.02651 87.94916 NA 88.47108 86.59288 78.96707 94.49507
[15] 85.21942 86.69626 84.42422 92.85615 85.09205 76.95736
> colMin(tmp5)
[1] 69.13249 61.46796 54.87432 62.59414 67.19973 54.90614 55.87786 58.99700
[9] 58.80155 NA 63.26806 56.62032 60.27974 55.51844 61.65051 55.16647
[17] 56.83312 52.93269 56.93576 59.94335
>
> Max(tmp5,na.rm=TRUE)
[1] 471.888
> Min(tmp5,na.rm=TRUE)
[1] 52.93269
> mean(tmp5,na.rm=TRUE)
[1] 73.50246
> Sum(tmp5,na.rm=TRUE)
[1] 14626.99
> Var(tmp5,na.rm=TRUE)
[1] 881.9049
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 88.43521 72.67335 75.52728 69.20182 69.72536 70.59007 72.59682 73.55107
[9] 73.03132 69.66875
> rowSums(tmp5,na.rm=TRUE)
[1] 1768.704 1453.467 1510.546 1384.036 1394.507 1411.801 1451.936 1471.021
[9] 1387.595 1393.375
> rowVars(tmp5,na.rm=TRUE)
[1] 8238.41695 43.60116 63.10485 74.15423 81.55860 53.06237
[7] 95.85426 92.80420 83.11033 69.34888
> rowSd(tmp5,na.rm=TRUE)
[1] 90.765726 6.603118 7.943856 8.611285 9.030980 7.284392 9.790519
[8] 9.633494 9.116486 8.327598
> rowMax(tmp5,na.rm=TRUE)
[1] 471.88797 82.80699 88.47108 85.77190 92.24189 81.64101 89.06324
[8] 90.84129 94.49507 87.58414
> rowMin(tmp5,na.rm=TRUE)
[1] 54.90614 58.47248 63.35070 54.87432 57.02413 56.83312 55.87786 56.24669
[9] 56.33430 52.93269
>
> colMeans(tmp5,na.rm=TRUE)
[1] 114.91103 73.97899 69.22263 71.27192 73.39669 67.84105 73.68707
[8] 75.71998 73.51435 70.71276 74.74490 73.69173 69.53766 71.12888
[15] 72.62643 68.37667 69.47641 66.59508 69.34440 69.99160
> colSums(tmp5,na.rm=TRUE)
[1] 1149.1103 739.7899 692.2263 712.7192 733.9669 678.4105 736.8707
[8] 757.1998 735.1435 636.4149 747.4490 736.9173 695.3766 711.2888
[15] 726.2643 683.7667 694.7641 665.9508 693.4440 699.9160
> colVars(tmp5,na.rm=TRUE)
[1] 15752.85358 58.99130 116.82443 41.67618 32.77550 113.96907
[7] 69.59512 61.27904 87.12523 99.20883 64.78614 73.54395
[13] 42.94654 136.79979 66.77462 87.84352 101.23438 126.14590
[19] 99.93107 38.93964
> colSd(tmp5,na.rm=TRUE)
[1] 125.510372 7.680580 10.808535 6.455709 5.724989 10.675630
[7] 8.342369 7.828093 9.334090 9.960363 8.048984 8.575777
[13] 6.553361 11.696144 8.171574 9.372487 10.061530 11.231469
[19] 9.996553 6.240163
> colMax(tmp5,na.rm=TRUE)
[1] 471.88797 90.84129 92.24189 82.19302 85.77190 89.06324 82.56907
[8] 87.02651 87.94916 87.58414 88.47108 86.59288 78.96707 94.49507
[15] 85.21942 86.69626 84.42422 92.85615 85.09205 76.95736
> colMin(tmp5,na.rm=TRUE)
[1] 69.13249 61.46796 54.87432 62.59414 67.19973 54.90614 55.87786 58.99700
[9] 58.80155 58.47248 63.26806 56.62032 60.27974 55.51844 61.65051 55.16647
[17] 56.83312 52.93269 56.93576 59.94335
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 88.43521 72.67335 75.52728 69.20182 69.72536 70.59007 72.59682 73.55107
[9] NaN 69.66875
> rowSums(tmp5,na.rm=TRUE)
[1] 1768.704 1453.467 1510.546 1384.036 1394.507 1411.801 1451.936 1471.021
[9] 0.000 1393.375
> rowVars(tmp5,na.rm=TRUE)
[1] 8238.41695 43.60116 63.10485 74.15423 81.55860 53.06237
[7] 95.85426 92.80420 NA 69.34888
> rowSd(tmp5,na.rm=TRUE)
[1] 90.765726 6.603118 7.943856 8.611285 9.030980 7.284392 9.790519
[8] 9.633494 NA 8.327598
> rowMax(tmp5,na.rm=TRUE)
[1] 471.88797 82.80699 88.47108 85.77190 92.24189 81.64101 89.06324
[8] 90.84129 NA 87.58414
> rowMin(tmp5,na.rm=TRUE)
[1] 54.90614 58.47248 63.35070 54.87432 57.02413 56.83312 55.87786 56.24669
[9] NA 52.93269
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 119.03685 73.77821 69.23375 71.53086 73.90746 67.79868 72.70018
[8] 75.23489 75.14911 NaN 75.11364 73.07549 68.73634 68.53263
[15] 72.53593 69.71472 68.56816 66.36969 68.20642 71.10807
> colSums(tmp5,na.rm=TRUE)
[1] 1071.3316 664.0039 623.1037 643.7777 665.1671 610.1881 654.3016
[8] 677.1140 676.3420 0.0000 676.0227 657.6794 618.6270 616.7937
[15] 652.8233 627.4324 617.1135 597.3272 613.8577 639.9727
> colVars(tmp5,na.rm=TRUE)
[1] 17530.45921 65.91173 131.42609 46.13142 33.93745 128.19502
[7] 67.33759 66.29173 67.95110 NA 71.35477 78.46474
[13] 41.09102 78.06938 75.02930 78.68245 104.60838 141.34261
[19] 97.85351 29.78385
> colSd(tmp5,na.rm=TRUE)
[1] 132.402641 8.118604 11.464122 6.792011 5.825586 11.322324
[7] 8.205948 8.141973 8.243246 NA 8.447175 8.858033
[13] 6.410228 8.835688 8.661946 8.870313 10.227824 11.888760
[19] 9.892093 5.457458
> colMax(tmp5,na.rm=TRUE)
[1] 471.88797 90.84129 92.24189 82.19302 85.77190 89.06324 82.39047
[8] 87.02651 87.94916 -Inf 88.47108 86.59288 78.96707 82.80699
[15] 85.21942 86.69626 84.42422 92.85615 85.09205 76.95736
> colMin(tmp5,na.rm=TRUE)
[1] 69.13249 61.46796 54.87432 62.59414 67.19973 54.90614 55.87786 58.99700
[9] 65.89797 Inf 63.26806 56.62032 60.27974 55.51844 61.65051 55.16647
[17] 56.83312 52.93269 56.93576 63.07850
>
>
>
>
> 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] 289.17451 167.35935 116.24169 252.75323 252.63930 114.34764 84.32995
[8] 105.26878 148.77995 246.61761
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 289.17451 167.35935 116.24169 252.75323 252.63930 114.34764 84.32995
[8] 105.26878 148.77995 246.61761
>
>
>
> 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] -1.136868e-13 0.000000e+00 -5.684342e-14 5.684342e-14 0.000000e+00
[6] -5.684342e-14 -1.421085e-14 5.684342e-14 1.136868e-13 0.000000e+00
[11] -7.815970e-14 3.126388e-13 2.842171e-14 -5.684342e-14 -5.684342e-14
[16] -1.421085e-13 5.684342e-14 2.842171e-14 -1.136868e-13 -5.684342e-14
>
>
>
>
>
>
>
>
>
>
> ## 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)
+ }
5 5
1 20
7 12
6 12
1 13
9 19
7 18
4 3
1 19
5 6
9 12
10 10
2 3
8 10
8 17
10 12
7 13
6 17
10 13
4 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] 2.714674
> Min(tmp)
[1] -2.302954
> mean(tmp)
[1] -0.04171153
> Sum(tmp)
[1] -4.171153
> Var(tmp)
[1] 0.8400069
>
> rowMeans(tmp)
[1] -0.04171153
> rowSums(tmp)
[1] -4.171153
> rowVars(tmp)
[1] 0.8400069
> rowSd(tmp)
[1] 0.9165189
> rowMax(tmp)
[1] 2.714674
> rowMin(tmp)
[1] -2.302954
>
> colMeans(tmp)
[1] -0.683520242 -0.196984893 1.037194322 -0.083482021 -0.810207903
[6] 0.818999906 0.209394405 0.316420556 -1.007313771 -1.477415241
[11] -0.384650018 1.798531309 0.401849308 0.471543231 -1.250646389
[16] 0.551215287 2.714674322 0.030041646 -0.222854408 0.367936897
[21] -0.252006799 -0.434340675 -0.297158765 -0.911624707 -1.125177213
[26] -1.015397283 0.937288929 -0.353567453 0.939109597 1.213105764
[31] -0.014435610 0.662507580 -1.306110611 -0.617001308 0.854291144
[36] -0.566013422 0.405990608 -0.585587978 0.775037219 -0.304198604
[41] -0.002519119 0.756062155 0.313626777 -0.482154491 1.052565934
[46] 0.426646146 0.350423163 -0.943449919 -1.269928085 0.221413397
[51] 1.450822809 0.521681130 -2.302953635 1.124907878 -1.922207320
[56] -0.107002197 -0.114616870 1.082189693 -0.257314022 -1.168678679
[61] -2.230906063 0.942608796 -1.485136950 -0.228432169 0.374726931
[66] -0.876898652 -0.105753193 1.052242906 -0.615791975 -0.846865173
[71] -0.287909070 -0.322693071 -1.508046967 0.352287603 -1.005854396
[76] 0.073218515 -0.267320068 0.470611101 1.148427391 0.218719559
[81] -0.925786504 0.583276358 0.407076274 -0.883130028 -1.550517327
[86] 1.896942581 -0.229093871 0.633106606 -0.323889296 -0.008864119
[91] 0.590645416 -0.054890353 -0.205757739 1.568274503 -0.483014169
[96] 0.660746275 -0.914849701 0.860272919 -0.946843946 0.968956830
> colSums(tmp)
[1] -0.683520242 -0.196984893 1.037194322 -0.083482021 -0.810207903
[6] 0.818999906 0.209394405 0.316420556 -1.007313771 -1.477415241
[11] -0.384650018 1.798531309 0.401849308 0.471543231 -1.250646389
[16] 0.551215287 2.714674322 0.030041646 -0.222854408 0.367936897
[21] -0.252006799 -0.434340675 -0.297158765 -0.911624707 -1.125177213
[26] -1.015397283 0.937288929 -0.353567453 0.939109597 1.213105764
[31] -0.014435610 0.662507580 -1.306110611 -0.617001308 0.854291144
[36] -0.566013422 0.405990608 -0.585587978 0.775037219 -0.304198604
[41] -0.002519119 0.756062155 0.313626777 -0.482154491 1.052565934
[46] 0.426646146 0.350423163 -0.943449919 -1.269928085 0.221413397
[51] 1.450822809 0.521681130 -2.302953635 1.124907878 -1.922207320
[56] -0.107002197 -0.114616870 1.082189693 -0.257314022 -1.168678679
[61] -2.230906063 0.942608796 -1.485136950 -0.228432169 0.374726931
[66] -0.876898652 -0.105753193 1.052242906 -0.615791975 -0.846865173
[71] -0.287909070 -0.322693071 -1.508046967 0.352287603 -1.005854396
[76] 0.073218515 -0.267320068 0.470611101 1.148427391 0.218719559
[81] -0.925786504 0.583276358 0.407076274 -0.883130028 -1.550517327
[86] 1.896942581 -0.229093871 0.633106606 -0.323889296 -0.008864119
[91] 0.590645416 -0.054890353 -0.205757739 1.568274503 -0.483014169
[96] 0.660746275 -0.914849701 0.860272919 -0.946843946 0.968956830
> 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] -0.683520242 -0.196984893 1.037194322 -0.083482021 -0.810207903
[6] 0.818999906 0.209394405 0.316420556 -1.007313771 -1.477415241
[11] -0.384650018 1.798531309 0.401849308 0.471543231 -1.250646389
[16] 0.551215287 2.714674322 0.030041646 -0.222854408 0.367936897
[21] -0.252006799 -0.434340675 -0.297158765 -0.911624707 -1.125177213
[26] -1.015397283 0.937288929 -0.353567453 0.939109597 1.213105764
[31] -0.014435610 0.662507580 -1.306110611 -0.617001308 0.854291144
[36] -0.566013422 0.405990608 -0.585587978 0.775037219 -0.304198604
[41] -0.002519119 0.756062155 0.313626777 -0.482154491 1.052565934
[46] 0.426646146 0.350423163 -0.943449919 -1.269928085 0.221413397
[51] 1.450822809 0.521681130 -2.302953635 1.124907878 -1.922207320
[56] -0.107002197 -0.114616870 1.082189693 -0.257314022 -1.168678679
[61] -2.230906063 0.942608796 -1.485136950 -0.228432169 0.374726931
[66] -0.876898652 -0.105753193 1.052242906 -0.615791975 -0.846865173
[71] -0.287909070 -0.322693071 -1.508046967 0.352287603 -1.005854396
[76] 0.073218515 -0.267320068 0.470611101 1.148427391 0.218719559
[81] -0.925786504 0.583276358 0.407076274 -0.883130028 -1.550517327
[86] 1.896942581 -0.229093871 0.633106606 -0.323889296 -0.008864119
[91] 0.590645416 -0.054890353 -0.205757739 1.568274503 -0.483014169
[96] 0.660746275 -0.914849701 0.860272919 -0.946843946 0.968956830
> colMin(tmp)
[1] -0.683520242 -0.196984893 1.037194322 -0.083482021 -0.810207903
[6] 0.818999906 0.209394405 0.316420556 -1.007313771 -1.477415241
[11] -0.384650018 1.798531309 0.401849308 0.471543231 -1.250646389
[16] 0.551215287 2.714674322 0.030041646 -0.222854408 0.367936897
[21] -0.252006799 -0.434340675 -0.297158765 -0.911624707 -1.125177213
[26] -1.015397283 0.937288929 -0.353567453 0.939109597 1.213105764
[31] -0.014435610 0.662507580 -1.306110611 -0.617001308 0.854291144
[36] -0.566013422 0.405990608 -0.585587978 0.775037219 -0.304198604
[41] -0.002519119 0.756062155 0.313626777 -0.482154491 1.052565934
[46] 0.426646146 0.350423163 -0.943449919 -1.269928085 0.221413397
[51] 1.450822809 0.521681130 -2.302953635 1.124907878 -1.922207320
[56] -0.107002197 -0.114616870 1.082189693 -0.257314022 -1.168678679
[61] -2.230906063 0.942608796 -1.485136950 -0.228432169 0.374726931
[66] -0.876898652 -0.105753193 1.052242906 -0.615791975 -0.846865173
[71] -0.287909070 -0.322693071 -1.508046967 0.352287603 -1.005854396
[76] 0.073218515 -0.267320068 0.470611101 1.148427391 0.218719559
[81] -0.925786504 0.583276358 0.407076274 -0.883130028 -1.550517327
[86] 1.896942581 -0.229093871 0.633106606 -0.323889296 -0.008864119
[91] 0.590645416 -0.054890353 -0.205757739 1.568274503 -0.483014169
[96] 0.660746275 -0.914849701 0.860272919 -0.946843946 0.968956830
> colMedians(tmp)
[1] -0.683520242 -0.196984893 1.037194322 -0.083482021 -0.810207903
[6] 0.818999906 0.209394405 0.316420556 -1.007313771 -1.477415241
[11] -0.384650018 1.798531309 0.401849308 0.471543231 -1.250646389
[16] 0.551215287 2.714674322 0.030041646 -0.222854408 0.367936897
[21] -0.252006799 -0.434340675 -0.297158765 -0.911624707 -1.125177213
[26] -1.015397283 0.937288929 -0.353567453 0.939109597 1.213105764
[31] -0.014435610 0.662507580 -1.306110611 -0.617001308 0.854291144
[36] -0.566013422 0.405990608 -0.585587978 0.775037219 -0.304198604
[41] -0.002519119 0.756062155 0.313626777 -0.482154491 1.052565934
[46] 0.426646146 0.350423163 -0.943449919 -1.269928085 0.221413397
[51] 1.450822809 0.521681130 -2.302953635 1.124907878 -1.922207320
[56] -0.107002197 -0.114616870 1.082189693 -0.257314022 -1.168678679
[61] -2.230906063 0.942608796 -1.485136950 -0.228432169 0.374726931
[66] -0.876898652 -0.105753193 1.052242906 -0.615791975 -0.846865173
[71] -0.287909070 -0.322693071 -1.508046967 0.352287603 -1.005854396
[76] 0.073218515 -0.267320068 0.470611101 1.148427391 0.218719559
[81] -0.925786504 0.583276358 0.407076274 -0.883130028 -1.550517327
[86] 1.896942581 -0.229093871 0.633106606 -0.323889296 -0.008864119
[91] 0.590645416 -0.054890353 -0.205757739 1.568274503 -0.483014169
[96] 0.660746275 -0.914849701 0.860272919 -0.946843946 0.968956830
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] -0.6835202 -0.1969849 1.037194 -0.08348202 -0.8102079 0.8189999 0.2093944
[2,] -0.6835202 -0.1969849 1.037194 -0.08348202 -0.8102079 0.8189999 0.2093944
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] 0.3164206 -1.007314 -1.477415 -0.38465 1.798531 0.4018493 0.4715432
[2,] 0.3164206 -1.007314 -1.477415 -0.38465 1.798531 0.4018493 0.4715432
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] -1.250646 0.5512153 2.714674 0.03004165 -0.2228544 0.3679369 -0.2520068
[2,] -1.250646 0.5512153 2.714674 0.03004165 -0.2228544 0.3679369 -0.2520068
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] -0.4343407 -0.2971588 -0.9116247 -1.125177 -1.015397 0.9372889 -0.3535675
[2,] -0.4343407 -0.2971588 -0.9116247 -1.125177 -1.015397 0.9372889 -0.3535675
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] 0.9391096 1.213106 -0.01443561 0.6625076 -1.306111 -0.6170013 0.8542911
[2,] 0.9391096 1.213106 -0.01443561 0.6625076 -1.306111 -0.6170013 0.8542911
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] -0.5660134 0.4059906 -0.585588 0.7750372 -0.3041986 -0.002519119 0.7560622
[2,] -0.5660134 0.4059906 -0.585588 0.7750372 -0.3041986 -0.002519119 0.7560622
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] 0.3136268 -0.4821545 1.052566 0.4266461 0.3504232 -0.9434499 -1.269928
[2,] 0.3136268 -0.4821545 1.052566 0.4266461 0.3504232 -0.9434499 -1.269928
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] 0.2214134 1.450823 0.5216811 -2.302954 1.124908 -1.922207 -0.1070022
[2,] 0.2214134 1.450823 0.5216811 -2.302954 1.124908 -1.922207 -0.1070022
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] -0.1146169 1.08219 -0.257314 -1.168679 -2.230906 0.9426088 -1.485137
[2,] -0.1146169 1.08219 -0.257314 -1.168679 -2.230906 0.9426088 -1.485137
[,64] [,65] [,66] [,67] [,68] [,69] [,70]
[1,] -0.2284322 0.3747269 -0.8768987 -0.1057532 1.052243 -0.615792 -0.8468652
[2,] -0.2284322 0.3747269 -0.8768987 -0.1057532 1.052243 -0.615792 -0.8468652
[,71] [,72] [,73] [,74] [,75] [,76] [,77]
[1,] -0.2879091 -0.3226931 -1.508047 0.3522876 -1.005854 0.07321851 -0.2673201
[2,] -0.2879091 -0.3226931 -1.508047 0.3522876 -1.005854 0.07321851 -0.2673201
[,78] [,79] [,80] [,81] [,82] [,83] [,84]
[1,] 0.4706111 1.148427 0.2187196 -0.9257865 0.5832764 0.4070763 -0.88313
[2,] 0.4706111 1.148427 0.2187196 -0.9257865 0.5832764 0.4070763 -0.88313
[,85] [,86] [,87] [,88] [,89] [,90] [,91]
[1,] -1.550517 1.896943 -0.2290939 0.6331066 -0.3238893 -0.008864119 0.5906454
[2,] -1.550517 1.896943 -0.2290939 0.6331066 -0.3238893 -0.008864119 0.5906454
[,92] [,93] [,94] [,95] [,96] [,97] [,98]
[1,] -0.05489035 -0.2057577 1.568275 -0.4830142 0.6607463 -0.9148497 0.8602729
[2,] -0.05489035 -0.2057577 1.568275 -0.4830142 0.6607463 -0.9148497 0.8602729
[,99] [,100]
[1,] -0.9468439 0.9689568
[2,] -0.9468439 0.9689568
>
>
> Max(tmp2)
[1] 2.58831
> Min(tmp2)
[1] -2.900436
> mean(tmp2)
[1] -0.04379215
> Sum(tmp2)
[1] -4.379215
> Var(tmp2)
[1] 1.007997
>
> rowMeans(tmp2)
[1] -0.89542092 1.68222089 0.36218232 -1.24270435 0.29422722 -0.96864321
[7] 0.66702331 0.49095038 -0.89385289 0.14632467 -0.01104149 -1.45331046
[13] 1.80099731 -0.22015507 0.36416021 1.12057849 -0.51304595 -0.99155871
[19] -1.06338466 0.61221137 -0.91991067 0.89616594 -1.91523426 1.31530616
[25] -2.19924316 1.48752075 0.09728947 0.33782648 -0.58748678 -0.50387679
[31] 0.50284828 0.02087629 -2.90043589 -1.06906238 0.55783101 -0.19159179
[37] -0.65363371 0.98455822 -2.10721534 1.63004055 -0.39580959 -0.74782108
[43] -0.93659362 -1.46725037 -0.34229311 1.12949181 -1.53661596 1.31020712
[49] 0.40631757 -0.42370772 -0.31590305 -0.06931714 1.16336014 -0.83141608
[55] 0.73909072 0.18756092 -0.26107436 -0.90094929 -0.37857070 -2.11306985
[61] -0.22533884 -0.88447184 -0.46846699 -1.19396928 0.71460396 -0.20139511
[67] -1.08782890 -0.86761499 1.37002349 1.04004899 0.38752001 0.10842255
[73] -0.62450805 -0.34051794 0.85250538 -0.21233705 1.04023162 1.10416427
[79] -1.06312415 1.16572885 1.03188811 1.47596382 -0.16972266 0.24368913
[85] -0.07563226 0.39545009 0.46036068 -0.61550267 1.08010171 0.61241220
[91] 1.17368744 -0.35228990 -0.64766473 0.24972879 -1.38929512 0.62887461
[97] 0.43185502 -0.58433832 0.18326605 2.58831001
> rowSums(tmp2)
[1] -0.89542092 1.68222089 0.36218232 -1.24270435 0.29422722 -0.96864321
[7] 0.66702331 0.49095038 -0.89385289 0.14632467 -0.01104149 -1.45331046
[13] 1.80099731 -0.22015507 0.36416021 1.12057849 -0.51304595 -0.99155871
[19] -1.06338466 0.61221137 -0.91991067 0.89616594 -1.91523426 1.31530616
[25] -2.19924316 1.48752075 0.09728947 0.33782648 -0.58748678 -0.50387679
[31] 0.50284828 0.02087629 -2.90043589 -1.06906238 0.55783101 -0.19159179
[37] -0.65363371 0.98455822 -2.10721534 1.63004055 -0.39580959 -0.74782108
[43] -0.93659362 -1.46725037 -0.34229311 1.12949181 -1.53661596 1.31020712
[49] 0.40631757 -0.42370772 -0.31590305 -0.06931714 1.16336014 -0.83141608
[55] 0.73909072 0.18756092 -0.26107436 -0.90094929 -0.37857070 -2.11306985
[61] -0.22533884 -0.88447184 -0.46846699 -1.19396928 0.71460396 -0.20139511
[67] -1.08782890 -0.86761499 1.37002349 1.04004899 0.38752001 0.10842255
[73] -0.62450805 -0.34051794 0.85250538 -0.21233705 1.04023162 1.10416427
[79] -1.06312415 1.16572885 1.03188811 1.47596382 -0.16972266 0.24368913
[85] -0.07563226 0.39545009 0.46036068 -0.61550267 1.08010171 0.61241220
[91] 1.17368744 -0.35228990 -0.64766473 0.24972879 -1.38929512 0.62887461
[97] 0.43185502 -0.58433832 0.18326605 2.58831001
> 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] -0.89542092 1.68222089 0.36218232 -1.24270435 0.29422722 -0.96864321
[7] 0.66702331 0.49095038 -0.89385289 0.14632467 -0.01104149 -1.45331046
[13] 1.80099731 -0.22015507 0.36416021 1.12057849 -0.51304595 -0.99155871
[19] -1.06338466 0.61221137 -0.91991067 0.89616594 -1.91523426 1.31530616
[25] -2.19924316 1.48752075 0.09728947 0.33782648 -0.58748678 -0.50387679
[31] 0.50284828 0.02087629 -2.90043589 -1.06906238 0.55783101 -0.19159179
[37] -0.65363371 0.98455822 -2.10721534 1.63004055 -0.39580959 -0.74782108
[43] -0.93659362 -1.46725037 -0.34229311 1.12949181 -1.53661596 1.31020712
[49] 0.40631757 -0.42370772 -0.31590305 -0.06931714 1.16336014 -0.83141608
[55] 0.73909072 0.18756092 -0.26107436 -0.90094929 -0.37857070 -2.11306985
[61] -0.22533884 -0.88447184 -0.46846699 -1.19396928 0.71460396 -0.20139511
[67] -1.08782890 -0.86761499 1.37002349 1.04004899 0.38752001 0.10842255
[73] -0.62450805 -0.34051794 0.85250538 -0.21233705 1.04023162 1.10416427
[79] -1.06312415 1.16572885 1.03188811 1.47596382 -0.16972266 0.24368913
[85] -0.07563226 0.39545009 0.46036068 -0.61550267 1.08010171 0.61241220
[91] 1.17368744 -0.35228990 -0.64766473 0.24972879 -1.38929512 0.62887461
[97] 0.43185502 -0.58433832 0.18326605 2.58831001
> rowMin(tmp2)
[1] -0.89542092 1.68222089 0.36218232 -1.24270435 0.29422722 -0.96864321
[7] 0.66702331 0.49095038 -0.89385289 0.14632467 -0.01104149 -1.45331046
[13] 1.80099731 -0.22015507 0.36416021 1.12057849 -0.51304595 -0.99155871
[19] -1.06338466 0.61221137 -0.91991067 0.89616594 -1.91523426 1.31530616
[25] -2.19924316 1.48752075 0.09728947 0.33782648 -0.58748678 -0.50387679
[31] 0.50284828 0.02087629 -2.90043589 -1.06906238 0.55783101 -0.19159179
[37] -0.65363371 0.98455822 -2.10721534 1.63004055 -0.39580959 -0.74782108
[43] -0.93659362 -1.46725037 -0.34229311 1.12949181 -1.53661596 1.31020712
[49] 0.40631757 -0.42370772 -0.31590305 -0.06931714 1.16336014 -0.83141608
[55] 0.73909072 0.18756092 -0.26107436 -0.90094929 -0.37857070 -2.11306985
[61] -0.22533884 -0.88447184 -0.46846699 -1.19396928 0.71460396 -0.20139511
[67] -1.08782890 -0.86761499 1.37002349 1.04004899 0.38752001 0.10842255
[73] -0.62450805 -0.34051794 0.85250538 -0.21233705 1.04023162 1.10416427
[79] -1.06312415 1.16572885 1.03188811 1.47596382 -0.16972266 0.24368913
[85] -0.07563226 0.39545009 0.46036068 -0.61550267 1.08010171 0.61241220
[91] 1.17368744 -0.35228990 -0.64766473 0.24972879 -1.38929512 0.62887461
[97] 0.43185502 -0.58433832 0.18326605 2.58831001
>
> colMeans(tmp2)
[1] -0.04379215
> colSums(tmp2)
[1] -4.379215
> colVars(tmp2)
[1] 1.007997
> colSd(tmp2)
[1] 1.003991
> colMax(tmp2)
[1] 2.58831
> colMin(tmp2)
[1] -2.900436
> colMedians(tmp2)
[1] -0.0724747
> colRanges(tmp2)
[,1]
[1,] -2.900436
[2,] 2.588310
>
> 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] -2.72317981 -5.84314904 3.48698900 0.07642964 3.91481985 1.17363427
[7] -1.84545243 4.26683802 -3.32916407 -0.30809588
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.7212911
[2,] -0.8622230
[3,] -0.3903711
[4,] 0.6779054
[5,] 1.2287594
>
> rowApply(tmp,sum)
[1] 0.2509511 -1.3651943 4.6034177 4.3381698 -1.2739232 3.0306378
[7] -0.2434297 -1.9228032 -3.7514208 -4.7967356
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 3 9 8 3 5 1 4 6 8 2
[2,] 2 7 10 7 2 2 2 3 1 4
[3,] 9 5 6 10 7 7 6 9 2 6
[4,] 6 1 2 9 6 6 10 4 10 3
[5,] 7 10 7 4 10 8 5 5 3 5
[6,] 10 6 5 2 1 4 7 8 9 7
[7,] 4 2 4 8 9 10 1 1 7 1
[8,] 5 4 9 5 8 5 9 10 5 9
[9,] 8 3 1 1 4 9 3 7 4 8
[10,] 1 8 3 6 3 3 8 2 6 10
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] 1.2098715 -0.5807554 -0.3784769 2.4398122 1.3361259 -0.4231125
[7] -1.6578149 -0.8714102 1.5457889 0.9303380 3.1861878 -2.2514976
[13] 1.8070893 2.7883610 -1.5546278 -0.2840500 -4.5921243 -0.9426186
[19] -2.4368884 5.2696157
> colApply(tmp,quantile)[,1]
[,1]
[1,] -0.99031968
[2,] -0.09092424
[3,] 0.26150929
[4,] 0.77289516
[5,] 1.25671094
>
> rowApply(tmp,sum)
[1] 2.2416765 -2.6996494 6.9533686 -0.6168469 -1.3387353
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 9 14 1 17 17
[2,] 10 3 13 5 19
[3,] 17 9 5 8 6
[4,] 20 7 16 4 11
[5,] 8 4 15 16 18
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] -0.09092424 -0.01230329 0.87792690 2.82710127 -0.2690234 -1.0801280
[2,] 0.26150929 -1.13593323 -0.10530682 -0.37679637 -1.0145960 0.0867326
[3,] -0.99031968 0.73877783 -0.37875401 1.17223370 0.8642966 -0.5976117
[4,] 1.25671094 -1.19121431 0.03675594 -1.21282726 0.9788860 0.6898499
[5,] 0.77289516 1.01991757 -0.80909889 0.03010081 0.7765628 0.4780446
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] 0.8030144 -1.33204580 0.81665295 0.57314569 1.3471895 -1.84174415
[2,] 0.2213436 1.18514805 0.79713834 -0.01446705 1.0328070 0.05974912
[3,] -0.4379283 0.05635531 -0.02988815 0.75821190 1.3513231 0.18455704
[4,] 0.2585881 0.16752329 0.15410823 -1.10625584 -0.8420232 0.19188508
[5,] -2.5028326 -0.94839109 -0.19222251 0.71970330 0.2968914 -0.84594470
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] -1.7126516 -0.27858750 0.02706978 -0.69188895 0.2033411 -0.4396578
[2,] 0.6740552 0.66732511 -0.89984426 -0.93437801 -2.9271917 -0.1621642
[3,] 0.3776804 -0.04901643 0.50904200 -0.29312368 1.4290793 -0.5441503
[4,] 0.3875415 1.69252417 -1.72236998 1.67098359 -1.9556562 0.8235152
[5,] 2.0804638 0.75611561 0.53147469 -0.03564297 -1.3416968 -0.6201614
[,19] [,20]
[1,] 0.3553198 2.1598699
[2,] -1.4587801 1.3440000
[3,] 1.6013084 1.2312953
[4,] -2.2822752 1.3869032
[5,] -0.6524613 -0.8524527
>
>
> is.BufferedMatrix(tmp)
[1] TRUE
>
> as.BufferedMatrix(as.matrix(tmp))
BufferedMatrix object
Matrix size: 5 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 800 bytes.
>
>
>
> subBufferedMatrix(tmp,1:5,1:5)
BufferedMatrix object
Matrix size: 5 5
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 650 bytes.
Disk usage : 200 bytes.
> subBufferedMatrix(tmp,,5:8)
BufferedMatrix object
Matrix size: 5 4
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 563 bytes.
Disk usage : 160 bytes.
> subBufferedMatrix(tmp,1:3,)
BufferedMatrix object
Matrix size: 3 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 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 0.1934011 -0.20482 0.188926 0.1606529 0.2054089 1.759902 0.3875711
col8 col9 col10 col11 col12 col13 col14
row1 -1.606671 0.2917463 1.494981 0.6706468 -0.3750023 0.9405331 0.8704078
col15 col16 col17 col18 col19 col20
row1 0.8748678 -0.4726115 -0.7050159 1.518867 -0.8376929 -1.17184
> tmp[,"col10"]
col10
row1 1.4949808
row2 1.1011131
row3 -1.0854886
row4 0.3961342
row5 -0.2185411
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7
row1 0.19340113 -0.204820 0.1889260 0.1606529 0.2054089 1.759902 0.3875711
row5 -0.03231321 1.818002 -0.2608069 -0.6544695 -1.2375637 -1.679428 1.4659425
col8 col9 col10 col11 col12 col13 col14
row1 -1.6066713 0.2917463 1.4949808 0.6706468 -0.3750023 0.9405331 0.87040775
row5 0.2401374 0.3315743 -0.2185411 2.1969685 0.7684198 0.3945635 0.09291032
col15 col16 col17 col18 col19 col20
row1 0.8748678 -0.4726115 -0.7050159 1.518867 -0.8376929 -1.171840
row5 -2.6980371 -2.1373403 -0.2370911 1.028361 -0.4814494 1.469433
> tmp[,c("col6","col20")]
col6 col20
row1 1.7599021 -1.17184041
row2 0.4612740 -0.01276909
row3 0.3573592 -1.33905784
row4 0.8805717 0.35203346
row5 -1.6794278 1.46943312
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 1.759902 -1.171840
row5 -1.679428 1.469433
>
>
>
>
> 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 49.07196 50.61604 49.75559 49.26426 51.17145 105.0494 52.03082 49.57173
col9 col10 col11 col12 col13 col14 col15 col16
row1 50.41376 50.16483 49.93733 50.39066 48.03511 49.06437 49.1699 49.46905
col17 col18 col19 col20
row1 52.00192 50.86644 50.64568 104.8047
> tmp[,"col10"]
col10
row1 50.16483
row2 28.15630
row3 27.70856
row4 28.34103
row5 49.47777
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 49.07196 50.61604 49.75559 49.26426 51.17145 105.0494 52.03082 49.57173
row5 50.03866 50.53460 49.93050 50.26634 50.02821 106.0700 49.18940 51.85755
col9 col10 col11 col12 col13 col14 col15 col16
row1 50.41376 50.16483 49.93733 50.39066 48.03511 49.06437 49.16990 49.46905
row5 49.05523 49.47777 50.30932 48.12130 50.98952 51.61648 49.78398 51.27581
col17 col18 col19 col20
row1 52.00192 50.86644 50.64568 104.8047
row5 50.35211 51.40325 47.47910 105.8152
> tmp[,c("col6","col20")]
col6 col20
row1 105.04939 104.80470
row2 75.57812 76.14171
row3 74.88063 74.71833
row4 74.67095 75.29897
row5 106.06997 105.81521
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 105.0494 104.8047
row5 106.0700 105.8152
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 105.0494 104.8047
row5 106.0700 105.8152
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] -0.1635774
[2,] -0.6409956
[3,] 0.2498226
[4,] 0.2048202
[5,] -1.1776115
> tmp[,c("col17","col7")]
col17 col7
[1,] -0.7430589 0.5257669
[2,] 0.3237765 0.5649578
[3,] 0.4392313 -1.6232815
[4,] 0.1790952 -0.3050759
[5,] -1.0362916 1.2985005
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] -0.38566406 0.1770210
[2,] 0.06181794 -1.1189186
[3,] -2.02660814 -0.5783127
[4,] 1.04882990 2.1331505
[5,] -1.59915202 -0.0979782
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] -0.3856641
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] -0.38566406
[2,] 0.06181794
>
>
>
> 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] [,7]
row3 1.384976 -0.9049220 1.92634298 -1.562183 -1.246256 -0.4478158 0.5485867
row1 1.559691 0.5785599 -0.05832194 -2.799075 -2.138543 -0.7663249 -0.7524659
[,8] [,9] [,10] [,11] [,12] [,13]
row3 0.176739 1.9563880 0.5044495 -0.0007020245 -0.9745769 0.6136514
row1 1.237478 0.2728682 -0.6359784 -0.1711813584 -0.7259023 -1.1259027
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
row3 1.607260 -0.9116881 -0.79027090 0.4528653 -0.6448934 1.279887 -0.3801278
row1 -1.606082 -1.6015070 -0.04750723 -2.5602686 0.1353618 0.935069 -1.9568299
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 1.877598 0.1086931 -0.8360896 0.4224377 0.2318264 -0.6360844 1.122323
[,8] [,9] [,10]
row2 -0.5005069 0.3079712 -1.157819
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6]
row5 -0.6042621 -1.100167 -0.3810907 -0.2590458 -1.554514 -0.7839662
[,7] [,8] [,9] [,10] [,11] [,12] [,13]
row5 -0.03918589 -0.8335793 -0.9017508 0.0550001 -1.35799 1.158277 -0.4529419
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
row5 1.796883 -0.9511023 -1.409213 0.1783782 -0.16733 0.1803087 -0.3892656
>
>
> 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: 0x60000161c060>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BMc28f60894424"
[2] "/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BMc28f53d8c8ff"
[3] "/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BMc28f3d74085a"
[4] "/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BMc28fcd06c3b"
[5] "/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BMc28f47719c0f"
[6] "/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BMc28f73bcc16d"
[7] "/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BMc28f6d3f1677"
[8] "/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BMc28f48dc16a9"
[9] "/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BMc28f6953d69d"
[10] "/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BMc28f7f2f1370"
[11] "/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BMc28f6ba55f4b"
[12] "/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BMc28f36136c23"
[13] "/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BMc28f35208991"
[14] "/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BMc28f6b27a9d6"
[15] "/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests/BMc28f78ff578f"
>
>
> ### 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: 0x6000016245a0>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x6000016245a0>
Warning message:
In dir.create(new.directory) :
'/Users/biocbuild/bbs-3.20-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x6000016245a0>
> rowMedians(tmp)
[1] 0.200816615 0.475608008 0.186441955 0.097321657 -0.514500498
[6] 0.274854981 -0.114587295 0.318761281 0.295508898 -0.311403690
[11] -0.023569620 0.261389047 -0.356933834 0.390994501 0.094520096
[16] -0.366646322 0.054757861 0.332690607 -0.057352141 0.007629569
[21] -0.228991749 -0.641721913 -0.032680351 0.107470501 -0.603632061
[26] 0.326389084 0.220015281 0.262440606 0.252966969 0.246353801
[31] -0.048120592 -0.235316260 0.391696427 0.543453786 -0.257280867
[36] 0.385760392 0.100600878 0.764680237 -0.293055139 -0.056760142
[41] 0.235294251 0.343369843 0.222536764 -0.068828715 0.368650472
[46] -0.664793572 -0.198079920 -0.457270697 0.170000131 -0.051125347
[51] -0.041192208 -0.215987441 -0.112652600 -0.049093419 0.462170071
[56] -0.520365361 0.324086428 -0.060189293 -0.375845528 0.409774161
[61] -0.220755340 -0.115707600 0.131726568 0.136232390 -0.265789374
[66] 0.147197163 -0.052239795 0.730925370 -0.023541779 -0.085244571
[71] 0.307411718 -0.166491860 0.681300477 -0.264790744 0.162956937
[76] -0.109499650 -0.338680620 0.207279754 -0.108668301 0.422552378
[81] -0.115101290 -0.360179936 0.353759603 -0.179036353 0.344223869
[86] -0.394067508 -0.204890429 0.475875944 -0.474294585 0.102949051
[91] -0.131216614 0.279391615 -0.132697151 -0.276626775 0.329298554
[96] 0.106069398 0.234128558 -0.204073478 0.018038271 0.247383302
[101] -0.238033588 -0.288892692 -0.045064546 0.361539874 0.504433481
[106] 0.137068038 -0.429221161 0.028445290 -0.499548943 -0.259919251
[111] 0.446365418 -0.149245961 -0.067738267 0.305360383 -0.319884436
[116] 0.424867372 -0.297615150 0.577061448 0.231073303 -0.033478596
[121] 0.191107368 0.146371010 0.316915758 0.284664064 0.175883261
[126] 0.250026729 0.155636261 0.207940934 0.162057688 -0.102121252
[131] 0.129722429 0.212392113 0.176059243 -0.405911646 0.472945345
[136] -0.206754737 -0.019136464 0.192735932 -0.297702454 0.037080355
[141] -0.643470274 -0.028213841 0.462780530 0.132030153 -0.018758996
[146] -0.635083190 -0.274255274 0.480607422 -0.306398979 -0.468709965
[151] 0.512661093 -0.298788917 -0.130295272 -0.121479490 -0.705372010
[156] 0.433664097 0.331913850 0.212551553 -0.114641955 -0.070000982
[161] 0.030629830 -0.200314151 0.227886406 0.122285019 -0.277492152
[166] 0.079133441 -0.047784388 0.351748430 0.389408939 0.063124557
[171] -0.129797120 -0.030952611 0.538349204 0.539139167 -0.294661151
[176] -0.437892391 -0.494008028 -0.257152687 -0.083082374 -0.188490891
[181] 0.277023258 -0.119381388 -0.061196095 -0.239312332 0.103508068
[186] -0.165698989 0.481835335 0.418918184 -0.066880205 0.910136272
[191] -0.071424203 -0.382724908 0.088198675 0.073255644 0.611459786
[196] 0.048859402 0.038963980 -0.074212586 0.249041404 -0.337564222
[201] 0.715950840 0.406863457 0.580763254 -0.728147497 0.633873427
[206] -0.134848931 -0.177554814 -0.005440487 0.672463872 -0.256917559
[211] -0.136967088 0.112230383 -0.212603722 -0.115010431 -0.537852017
[216] -0.216448979 -0.042370217 0.147874269 0.150007541 0.067011504
[221] 0.080990216 -0.418490637 -0.179468982 -0.190526407 -0.036382832
[226] 0.274260233 0.189489888 0.179852130 -0.497220828 -0.014188502
>
> proc.time()
user system elapsed
5.177 18.965 29.173
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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: 0x600003510000>
> .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: 0x600003510000>
> .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: 0x600003510000>
> .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: 0x600003510000>
> 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: 0x60000353c0c0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x60000353c0c0>
> .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: 0x60000353c0c0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x60000353c0c0>
> .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: 0x60000353c0c0>
> 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: 0x600003564000>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003564000>
> .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: 0x600003564000>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x600003564000>
> .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: 0x600003564000>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x600003564000>
> .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: 0x600003564000>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x600003564000>
> .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: 0x600003564000>
> 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: 0x600003560000>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x600003560000>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003560000>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003560000>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFilec941172c7234" "BufferedMatrixFilec94166fdbfce"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFilec941172c7234" "BufferedMatrixFilec94166fdbfce"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003560240>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003560240>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x600003560240>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x600003560240>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x600003560240>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x600003560240>
> .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: 0x600003528060>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003528060>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x600003528060>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x600003528060>
> 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: 0x6000035281e0>
> .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: 0x6000035281e0>
> rm(P)
>
> proc.time()
user system elapsed
0.603 0.226 0.976
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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
>
> Temp <- createBufferedMatrix(100)
> dim(Temp)
[1] 100 0
> buffer.dim(Temp)
[1] 1 1
>
>
> proc.time()
user system elapsed
0.601 0.143 0.763