Ben Bolstad
| Snapshot Date: 2026-01-12 13:45 -0500 (Mon, 12 Jan 2026) |
| git_url: https://git.bioconductor.org/packages/BufferedMatrix |
| git_branch: RELEASE_3_22 |
| git_last_commit: d2ce144 |
| git_last_commit_date: 2025-10-29 09:58:55 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-01-15 11:59 -0500 (Thu, 15 Jan 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4886 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4672 |
| 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 257/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BufferedMatrix 1.74.0 (landing page) Ben Bolstad
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: BufferedMatrix |
| Version: 1.74.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BufferedMatrix_1.74.0.tar.gz |
| StartedAt: 2026-01-13 07:11:33 -0000 (Tue, 13 Jan 2026) |
| EndedAt: 2026-01-13 07:12:04 -0000 (Tue, 13 Jan 2026) |
| EllapsedTime: 31.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BufferedMatrix.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BufferedMatrix_1.74.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BufferedMatrix/DESCRIPTION’ ... OK
* this is package ‘BufferedMatrix’ version ‘1.74.0’
* 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 ... OK
* used C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
* 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 loading without being on the library search path ... 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 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
‘/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/00check.log’
for details.
BufferedMatrix.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD INSTALL BufferedMatrix
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘BufferedMatrix’ ...
** this is package ‘BufferedMatrix’ version ‘1.74.0’
** using staged installation
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c RBufferedMatrix.c -o RBufferedMatrix.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -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){
| ^~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c doubleBufferedMatrix_C_tests.c -o doubleBufferedMatrix_C_tests.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c init_package.c -o init_package.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -shared -L/home/biocbuild/R/R-4.5.0/lib -L/usr/local/lib -o BufferedMatrix.so RBufferedMatrix.o doubleBufferedMatrix.o doubleBufferedMatrix_C_tests.o init_package.o -L/home/biocbuild/R/R-4.5.0/lib -lR
installing to /home/biocbuild/R/R-4.5.0/site-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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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
0.337 0.028 0.350
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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] "/home/biocbuild/bbs-3.22-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 478398 25.6 1047041 56 639620 34.2
Vcells 885166 6.8 8388608 64 2080985 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 Jan 13 07:11:58 2026"
> 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 Jan 13 07:11:58 2026"
>
>
> 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: 0xddacff0>
>
>
>
> 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 Jan 13 07:11:59 2026"
> 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 Jan 13 07:11:59 2026"
>
> ColMode(tmp2)
<pointer: 0xddacff0>
>
>
>
> ### 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,] 100.6365967 0.9933780 1.27563044 -0.5116524
[2,] -0.1012668 -0.4808680 0.02697948 0.0574561
[3,] 1.2833184 -0.3413942 -1.75801420 -1.3856293
[4,] 0.3263259 0.2374469 0.63922752 -0.5428366
> ewApply(tmp5,abs)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 2 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 100.6365967 0.9933780 1.27563044 0.5116524
[2,] 0.1012668 0.4808680 0.02697948 0.0574561
[3,] 1.2833184 0.3413942 1.75801420 1.3856293
[4,] 0.3263259 0.2374469 0.63922752 0.5428366
> ewApply(tmp5,sqrt)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 2 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 10.0317793 0.9966835 1.1294381 0.7152988
[2,] 0.3182245 0.6934465 0.1642543 0.2397000
[3,] 1.1328365 0.5842895 1.3259013 1.1771275
[4,] 0.5712494 0.4872852 0.7995171 0.7367744
>
> 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: /home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 2 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 225.95439 35.96021 37.57001 32.66464
[2,] 28.28351 32.41533 26.66952 27.45446
[3,] 37.61168 31.18429 40.01703 38.15690
[4,] 31.03882 30.11030 33.63440 32.91058
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0xca8f6c0>
> exp(tmp5)
<pointer: 0xca8f6c0>
> log(tmp5,2)
<pointer: 0xca8f6c0>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 470.2945
> Min(tmp5)
[1] 53.54742
> mean(tmp5)
[1] 72.13805
> Sum(tmp5)
[1] 14427.61
> Var(tmp5)
[1] 867.4608
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 89.30439 67.10264 71.10593 68.73903 68.62112 68.37184 72.73861 68.83523
[9] 74.57196 71.98978
> rowSums(tmp5)
[1] 1786.088 1342.053 1422.119 1374.781 1372.422 1367.437 1454.772 1376.705
[9] 1491.439 1439.796
> rowVars(tmp5)
[1] 8102.41047 51.01672 71.70654 55.96656 64.30966 59.22574
[7] 71.52145 87.42123 57.17918 68.51524
> rowSd(tmp5)
[1] 90.013390 7.142599 8.467971 7.481080 8.019330 7.695826 8.457036
[8] 9.349932 7.561692 8.277393
> rowMax(tmp5)
[1] 470.29446 78.66180 83.29020 87.20167 82.44823 86.67102 86.85357
[8] 89.43777 89.07536 85.87878
> rowMin(tmp5)
[1] 57.52664 55.50912 57.98241 55.98073 53.54742 58.46627 55.99639 55.48510
[9] 54.36131 56.84671
>
> colMeans(tmp5)
[1] 106.65292 75.14132 68.29067 72.67654 74.67136 66.61059 68.85578
[8] 72.42768 69.59137 68.85231 69.44785 72.08919 71.70902 65.84892
[15] 66.48190 70.97058 71.17995 66.38595 70.60029 74.27689
> colSums(tmp5)
[1] 1066.5292 751.4132 682.9067 726.7654 746.7136 666.1059 688.5578
[8] 724.2768 695.9137 688.5231 694.4785 720.8919 717.0902 658.4892
[15] 664.8190 709.7058 711.7995 663.8595 706.0029 742.7689
> colVars(tmp5)
[1] 16379.06651 57.99569 86.07064 82.34446 79.79014 56.96909
[7] 24.02731 91.17393 40.85854 88.93714 50.98904 85.35409
[13] 99.94264 36.81749 79.02804 30.41071 73.94462 84.05183
[19] 58.83064 36.39246
> colSd(tmp5)
[1] 127.980727 7.615490 9.277427 9.074385 8.932533 7.547787
[7] 4.901766 9.548504 6.392069 9.430649 7.140661 9.238728
[13] 9.997132 6.067742 8.889772 5.514591 8.599106 9.167979
[19] 7.670113 6.032616
> colMax(tmp5)
[1] 470.29446 83.20906 83.29020 86.67102 89.07536 76.37685 74.89993
[8] 89.43777 80.62782 87.20167 78.66180 84.82449 86.85357 73.60222
[15] 84.67102 77.62939 82.80627 86.54893 81.57922 85.81158
> colMin(tmp5)
[1] 56.39160 62.67064 55.50912 57.14285 60.01966 53.54742 61.66110 57.84798
[9] 61.84366 57.12464 57.52664 55.99639 57.67071 56.84671 54.36131 63.84643
[17] 61.05509 56.27287 55.48510 66.45440
>
>
> ### 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] 89.30439 67.10264 71.10593 68.73903 68.62112 68.37184 72.73861 68.83523
[9] 74.57196 NA
> rowSums(tmp5)
[1] 1786.088 1342.053 1422.119 1374.781 1372.422 1367.437 1454.772 1376.705
[9] 1491.439 NA
> rowVars(tmp5)
[1] 8102.41047 51.01672 71.70654 55.96656 64.30966 59.22574
[7] 71.52145 87.42123 57.17918 65.47974
> rowSd(tmp5)
[1] 90.013390 7.142599 8.467971 7.481080 8.019330 7.695826 8.457036
[8] 9.349932 7.561692 8.091955
> rowMax(tmp5)
[1] 470.29446 78.66180 83.29020 87.20167 82.44823 86.67102 86.85357
[8] 89.43777 89.07536 NA
> rowMin(tmp5)
[1] 57.52664 55.50912 57.98241 55.98073 53.54742 58.46627 55.99639 55.48510
[9] 54.36131 NA
>
> colMeans(tmp5)
[1] 106.65292 75.14132 68.29067 72.67654 74.67136 66.61059 68.85578
[8] 72.42768 69.59137 68.85231 69.44785 72.08919 71.70902 65.84892
[15] 66.48190 70.97058 NA 66.38595 70.60029 74.27689
> colSums(tmp5)
[1] 1066.5292 751.4132 682.9067 726.7654 746.7136 666.1059 688.5578
[8] 724.2768 695.9137 688.5231 694.4785 720.8919 717.0902 658.4892
[15] 664.8190 709.7058 NA 663.8595 706.0029 742.7689
> colVars(tmp5)
[1] 16379.06651 57.99569 86.07064 82.34446 79.79014 56.96909
[7] 24.02731 91.17393 40.85854 88.93714 50.98904 85.35409
[13] 99.94264 36.81749 79.02804 30.41071 NA 84.05183
[19] 58.83064 36.39246
> colSd(tmp5)
[1] 127.980727 7.615490 9.277427 9.074385 8.932533 7.547787
[7] 4.901766 9.548504 6.392069 9.430649 7.140661 9.238728
[13] 9.997132 6.067742 8.889772 5.514591 NA 9.167979
[19] 7.670113 6.032616
> colMax(tmp5)
[1] 470.29446 83.20906 83.29020 86.67102 89.07536 76.37685 74.89993
[8] 89.43777 80.62782 87.20167 78.66180 84.82449 86.85357 73.60222
[15] 84.67102 77.62939 NA 86.54893 81.57922 85.81158
> colMin(tmp5)
[1] 56.39160 62.67064 55.50912 57.14285 60.01966 53.54742 61.66110 57.84798
[9] 61.84366 57.12464 57.52664 55.99639 57.67071 56.84671 54.36131 63.84643
[17] NA 56.27287 55.48510 66.45440
>
> Max(tmp5,na.rm=TRUE)
[1] 470.2945
> Min(tmp5,na.rm=TRUE)
[1] 53.54742
> mean(tmp5,na.rm=TRUE)
[1] 72.08445
> Sum(tmp5,na.rm=TRUE)
[1] 14344.8
> Var(tmp5,na.rm=TRUE)
[1] 871.2642
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 89.30439 67.10264 71.10593 68.73903 68.62112 68.37184 72.73861 68.83523
[9] 74.57196 71.42049
> rowSums(tmp5,na.rm=TRUE)
[1] 1786.088 1342.053 1422.119 1374.781 1372.422 1367.437 1454.772 1376.705
[9] 1491.439 1356.989
> rowVars(tmp5,na.rm=TRUE)
[1] 8102.41047 51.01672 71.70654 55.96656 64.30966 59.22574
[7] 71.52145 87.42123 57.17918 65.47974
> rowSd(tmp5,na.rm=TRUE)
[1] 90.013390 7.142599 8.467971 7.481080 8.019330 7.695826 8.457036
[8] 9.349932 7.561692 8.091955
> rowMax(tmp5,na.rm=TRUE)
[1] 470.29446 78.66180 83.29020 87.20167 82.44823 86.67102 86.85357
[8] 89.43777 89.07536 85.87878
> rowMin(tmp5,na.rm=TRUE)
[1] 57.52664 55.50912 57.98241 55.98073 53.54742 58.46627 55.99639 55.48510
[9] 54.36131 56.84671
>
> colMeans(tmp5,na.rm=TRUE)
[1] 106.65292 75.14132 68.29067 72.67654 74.67136 66.61059 68.85578
[8] 72.42768 69.59137 68.85231 69.44785 72.08919 71.70902 65.84892
[15] 66.48190 70.97058 69.88814 66.38595 70.60029 74.27689
> colSums(tmp5,na.rm=TRUE)
[1] 1066.5292 751.4132 682.9067 726.7654 746.7136 666.1059 688.5578
[8] 724.2768 695.9137 688.5231 694.4785 720.8919 717.0902 658.4892
[15] 664.8190 709.7058 628.9933 663.8595 706.0029 742.7689
> colVars(tmp5,na.rm=TRUE)
[1] 16379.06651 57.99569 86.07064 82.34446 79.79014 56.96909
[7] 24.02731 91.17393 40.85854 88.93714 50.98904 85.35409
[13] 99.94264 36.81749 79.02804 30.41071 64.41390 84.05183
[19] 58.83064 36.39246
> colSd(tmp5,na.rm=TRUE)
[1] 127.980727 7.615490 9.277427 9.074385 8.932533 7.547787
[7] 4.901766 9.548504 6.392069 9.430649 7.140661 9.238728
[13] 9.997132 6.067742 8.889772 5.514591 8.025827 9.167979
[19] 7.670113 6.032616
> colMax(tmp5,na.rm=TRUE)
[1] 470.29446 83.20906 83.29020 86.67102 89.07536 76.37685 74.89993
[8] 89.43777 80.62782 87.20167 78.66180 84.82449 86.85357 73.60222
[15] 84.67102 77.62939 81.85682 86.54893 81.57922 85.81158
> colMin(tmp5,na.rm=TRUE)
[1] 56.39160 62.67064 55.50912 57.14285 60.01966 53.54742 61.66110 57.84798
[9] 61.84366 57.12464 57.52664 55.99639 57.67071 56.84671 54.36131 63.84643
[17] 61.05509 56.27287 55.48510 66.45440
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 89.30439 67.10264 71.10593 68.73903 68.62112 68.37184 72.73861 68.83523
[9] 74.57196 NaN
> rowSums(tmp5,na.rm=TRUE)
[1] 1786.088 1342.053 1422.119 1374.781 1372.422 1367.437 1454.772 1376.705
[9] 1491.439 0.000
> rowVars(tmp5,na.rm=TRUE)
[1] 8102.41047 51.01672 71.70654 55.96656 64.30966 59.22574
[7] 71.52145 87.42123 57.17918 NA
> rowSd(tmp5,na.rm=TRUE)
[1] 90.013390 7.142599 8.467971 7.481080 8.019330 7.695826 8.457036
[8] 9.349932 7.561692 NA
> rowMax(tmp5,na.rm=TRUE)
[1] 470.29446 78.66180 83.29020 87.20167 82.44823 86.67102 86.85357
[8] 89.43777 89.07536 NA
> rowMin(tmp5,na.rm=TRUE)
[1] 57.52664 55.50912 57.98241 55.98073 53.54742 58.46627 55.99639 55.48510
[9] 54.36131 NA
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 110.19371 75.02259 67.85138 72.65200 73.92754 67.35527 68.18421
[8] 70.93311 69.56384 67.76912 70.61574 73.27732 72.73672 66.84917
[15] 66.11169 70.35990 NaN 65.77572 70.22195 73.80146
> colSums(tmp5,na.rm=TRUE)
[1] 991.7434 675.2033 610.6624 653.8680 665.3479 606.1974 613.6579 638.3980
[9] 626.0745 609.9221 635.5417 659.4959 654.6305 601.6425 595.0052 633.2391
[17] 0.0000 591.9815 631.9976 664.2132
> colVars(tmp5,na.rm=TRUE)
[1] 18285.40653 65.08655 94.65844 92.63074 83.53969 57.85170
[7] 21.95688 77.44121 45.95733 86.85467 42.01789 80.14236
[13] 100.55354 30.16416 87.36464 30.01665 NA 90.36912
[19] 64.57413 38.39873
> colSd(tmp5,na.rm=TRUE)
[1] 135.223543 8.067623 9.729257 9.624486 9.140005 7.606031
[7] 4.685817 8.800069 6.779184 9.319586 6.482121 8.952226
[13] 10.027639 5.492191 9.346906 5.478745 NA 9.506267
[19] 8.035803 6.196671
> colMax(tmp5,na.rm=TRUE)
[1] 470.29446 83.20906 83.29020 86.67102 89.07536 76.37685 74.68131
[8] 89.43777 80.62782 87.20167 78.66180 84.82449 86.85357 73.60222
[15] 84.67102 77.62939 -Inf 86.54893 81.57922 85.81158
> colMin(tmp5,na.rm=TRUE)
[1] 56.39160 62.67064 55.50912 57.14285 60.01966 53.54742 61.66110 57.84798
[9] 61.84366 57.12464 57.52664 55.99639 57.67071 57.98241 54.36131 63.84643
[17] Inf 56.27287 55.48510 66.45440
>
>
>
>
> 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] 169.2738 136.0078 111.7281 175.4053 124.4299 159.7091 249.1304 116.6018
[9] 248.0866 271.0258
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 169.2738 136.0078 111.7281 175.4053 124.4299 159.7091 249.1304 116.6018
[9] 248.0866 271.0258
>
>
>
> 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] -5.684342e-14 -1.136868e-13 5.684342e-14 5.684342e-14 -5.684342e-14
[6] 0.000000e+00 -1.136868e-13 0.000000e+00 0.000000e+00 5.684342e-14
[11] -2.842171e-13 8.526513e-14 0.000000e+00 -1.705303e-13 -8.526513e-14
[16] 1.136868e-13 1.136868e-13 5.684342e-14 -1.136868e-13 6.394885e-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)
+ }
8 20
10 10
7 5
10 13
6 8
5 9
9 2
9 7
7 16
9 19
9 7
4 13
7 2
9 5
8 5
6 13
10 9
1 19
5 15
6 8
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] 2.321952
> Min(tmp)
[1] -2.374874
> mean(tmp)
[1] -0.0284471
> Sum(tmp)
[1] -2.84471
> Var(tmp)
[1] 1.14622
>
> rowMeans(tmp)
[1] -0.0284471
> rowSums(tmp)
[1] -2.84471
> rowVars(tmp)
[1] 1.14622
> rowSd(tmp)
[1] 1.070617
> rowMax(tmp)
[1] 2.321952
> rowMin(tmp)
[1] -2.374874
>
> colMeans(tmp)
[1] 0.488327909 1.809075757 0.502131333 -2.080455377 -0.402487452
[6] -0.763466630 0.678738818 -1.883183564 -1.444882454 0.403600885
[11] -0.171818226 -0.463104918 -1.292100096 -0.903220249 -1.298924988
[16] 1.179357773 -1.989594127 0.151993410 1.051852689 0.430268190
[21] -2.038076607 -1.589470690 1.025279223 0.882115898 0.109217326
[26] 1.617014134 1.384028945 -1.128694446 0.312621485 -0.673670734
[31] 1.808087430 0.075940096 -1.302130194 0.124071230 1.771586759
[36] 0.858966457 1.079339869 1.579590398 -0.519575395 -1.401497286
[41] 0.286697636 0.458495551 0.705569326 -1.134437814 0.388301178
[46] 0.550579853 -1.529233562 1.095672360 -0.405931023 0.253274754
[51] -0.250470175 1.177971782 -0.531891611 -0.430115172 0.912553259
[56] -1.705985447 0.769897316 -0.789571114 -0.804030424 -0.168922666
[61] 0.224964432 -0.187192182 -1.126238175 0.806789532 0.157070099
[66] 0.600244851 0.558459778 1.262219066 -1.646461601 0.120047124
[71] 0.982481998 0.652021513 1.441312883 -1.300500247 -2.292701460
[76] 0.138833987 0.264266871 0.733370278 -0.015091662 -2.374873696
[81] -0.009218994 2.321952381 0.617460777 -1.063587996 -0.702480860
[86] -0.108550173 1.781460533 1.201111945 -0.726483429 -0.603328118
[91] -0.437027716 -0.023304659 0.308282099 0.907619388 -1.800698096
[96] 1.341899693 -0.836067335 -0.268143455 0.022859623 -0.592766008
> colSums(tmp)
[1] 0.488327909 1.809075757 0.502131333 -2.080455377 -0.402487452
[6] -0.763466630 0.678738818 -1.883183564 -1.444882454 0.403600885
[11] -0.171818226 -0.463104918 -1.292100096 -0.903220249 -1.298924988
[16] 1.179357773 -1.989594127 0.151993410 1.051852689 0.430268190
[21] -2.038076607 -1.589470690 1.025279223 0.882115898 0.109217326
[26] 1.617014134 1.384028945 -1.128694446 0.312621485 -0.673670734
[31] 1.808087430 0.075940096 -1.302130194 0.124071230 1.771586759
[36] 0.858966457 1.079339869 1.579590398 -0.519575395 -1.401497286
[41] 0.286697636 0.458495551 0.705569326 -1.134437814 0.388301178
[46] 0.550579853 -1.529233562 1.095672360 -0.405931023 0.253274754
[51] -0.250470175 1.177971782 -0.531891611 -0.430115172 0.912553259
[56] -1.705985447 0.769897316 -0.789571114 -0.804030424 -0.168922666
[61] 0.224964432 -0.187192182 -1.126238175 0.806789532 0.157070099
[66] 0.600244851 0.558459778 1.262219066 -1.646461601 0.120047124
[71] 0.982481998 0.652021513 1.441312883 -1.300500247 -2.292701460
[76] 0.138833987 0.264266871 0.733370278 -0.015091662 -2.374873696
[81] -0.009218994 2.321952381 0.617460777 -1.063587996 -0.702480860
[86] -0.108550173 1.781460533 1.201111945 -0.726483429 -0.603328118
[91] -0.437027716 -0.023304659 0.308282099 0.907619388 -1.800698096
[96] 1.341899693 -0.836067335 -0.268143455 0.022859623 -0.592766008
> 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] 0.488327909 1.809075757 0.502131333 -2.080455377 -0.402487452
[6] -0.763466630 0.678738818 -1.883183564 -1.444882454 0.403600885
[11] -0.171818226 -0.463104918 -1.292100096 -0.903220249 -1.298924988
[16] 1.179357773 -1.989594127 0.151993410 1.051852689 0.430268190
[21] -2.038076607 -1.589470690 1.025279223 0.882115898 0.109217326
[26] 1.617014134 1.384028945 -1.128694446 0.312621485 -0.673670734
[31] 1.808087430 0.075940096 -1.302130194 0.124071230 1.771586759
[36] 0.858966457 1.079339869 1.579590398 -0.519575395 -1.401497286
[41] 0.286697636 0.458495551 0.705569326 -1.134437814 0.388301178
[46] 0.550579853 -1.529233562 1.095672360 -0.405931023 0.253274754
[51] -0.250470175 1.177971782 -0.531891611 -0.430115172 0.912553259
[56] -1.705985447 0.769897316 -0.789571114 -0.804030424 -0.168922666
[61] 0.224964432 -0.187192182 -1.126238175 0.806789532 0.157070099
[66] 0.600244851 0.558459778 1.262219066 -1.646461601 0.120047124
[71] 0.982481998 0.652021513 1.441312883 -1.300500247 -2.292701460
[76] 0.138833987 0.264266871 0.733370278 -0.015091662 -2.374873696
[81] -0.009218994 2.321952381 0.617460777 -1.063587996 -0.702480860
[86] -0.108550173 1.781460533 1.201111945 -0.726483429 -0.603328118
[91] -0.437027716 -0.023304659 0.308282099 0.907619388 -1.800698096
[96] 1.341899693 -0.836067335 -0.268143455 0.022859623 -0.592766008
> colMin(tmp)
[1] 0.488327909 1.809075757 0.502131333 -2.080455377 -0.402487452
[6] -0.763466630 0.678738818 -1.883183564 -1.444882454 0.403600885
[11] -0.171818226 -0.463104918 -1.292100096 -0.903220249 -1.298924988
[16] 1.179357773 -1.989594127 0.151993410 1.051852689 0.430268190
[21] -2.038076607 -1.589470690 1.025279223 0.882115898 0.109217326
[26] 1.617014134 1.384028945 -1.128694446 0.312621485 -0.673670734
[31] 1.808087430 0.075940096 -1.302130194 0.124071230 1.771586759
[36] 0.858966457 1.079339869 1.579590398 -0.519575395 -1.401497286
[41] 0.286697636 0.458495551 0.705569326 -1.134437814 0.388301178
[46] 0.550579853 -1.529233562 1.095672360 -0.405931023 0.253274754
[51] -0.250470175 1.177971782 -0.531891611 -0.430115172 0.912553259
[56] -1.705985447 0.769897316 -0.789571114 -0.804030424 -0.168922666
[61] 0.224964432 -0.187192182 -1.126238175 0.806789532 0.157070099
[66] 0.600244851 0.558459778 1.262219066 -1.646461601 0.120047124
[71] 0.982481998 0.652021513 1.441312883 -1.300500247 -2.292701460
[76] 0.138833987 0.264266871 0.733370278 -0.015091662 -2.374873696
[81] -0.009218994 2.321952381 0.617460777 -1.063587996 -0.702480860
[86] -0.108550173 1.781460533 1.201111945 -0.726483429 -0.603328118
[91] -0.437027716 -0.023304659 0.308282099 0.907619388 -1.800698096
[96] 1.341899693 -0.836067335 -0.268143455 0.022859623 -0.592766008
> colMedians(tmp)
[1] 0.488327909 1.809075757 0.502131333 -2.080455377 -0.402487452
[6] -0.763466630 0.678738818 -1.883183564 -1.444882454 0.403600885
[11] -0.171818226 -0.463104918 -1.292100096 -0.903220249 -1.298924988
[16] 1.179357773 -1.989594127 0.151993410 1.051852689 0.430268190
[21] -2.038076607 -1.589470690 1.025279223 0.882115898 0.109217326
[26] 1.617014134 1.384028945 -1.128694446 0.312621485 -0.673670734
[31] 1.808087430 0.075940096 -1.302130194 0.124071230 1.771586759
[36] 0.858966457 1.079339869 1.579590398 -0.519575395 -1.401497286
[41] 0.286697636 0.458495551 0.705569326 -1.134437814 0.388301178
[46] 0.550579853 -1.529233562 1.095672360 -0.405931023 0.253274754
[51] -0.250470175 1.177971782 -0.531891611 -0.430115172 0.912553259
[56] -1.705985447 0.769897316 -0.789571114 -0.804030424 -0.168922666
[61] 0.224964432 -0.187192182 -1.126238175 0.806789532 0.157070099
[66] 0.600244851 0.558459778 1.262219066 -1.646461601 0.120047124
[71] 0.982481998 0.652021513 1.441312883 -1.300500247 -2.292701460
[76] 0.138833987 0.264266871 0.733370278 -0.015091662 -2.374873696
[81] -0.009218994 2.321952381 0.617460777 -1.063587996 -0.702480860
[86] -0.108550173 1.781460533 1.201111945 -0.726483429 -0.603328118
[91] -0.437027716 -0.023304659 0.308282099 0.907619388 -1.800698096
[96] 1.341899693 -0.836067335 -0.268143455 0.022859623 -0.592766008
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] 0.4883279 1.809076 0.5021313 -2.080455 -0.4024875 -0.7634666 0.6787388
[2,] 0.4883279 1.809076 0.5021313 -2.080455 -0.4024875 -0.7634666 0.6787388
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] -1.883184 -1.444882 0.4036009 -0.1718182 -0.4631049 -1.2921 -0.9032202
[2,] -1.883184 -1.444882 0.4036009 -0.1718182 -0.4631049 -1.2921 -0.9032202
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] -1.298925 1.179358 -1.989594 0.1519934 1.051853 0.4302682 -2.038077
[2,] -1.298925 1.179358 -1.989594 0.1519934 1.051853 0.4302682 -2.038077
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] -1.589471 1.025279 0.8821159 0.1092173 1.617014 1.384029 -1.128694
[2,] -1.589471 1.025279 0.8821159 0.1092173 1.617014 1.384029 -1.128694
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] 0.3126215 -0.6736707 1.808087 0.0759401 -1.30213 0.1240712 1.771587
[2,] 0.3126215 -0.6736707 1.808087 0.0759401 -1.30213 0.1240712 1.771587
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] 0.8589665 1.07934 1.57959 -0.5195754 -1.401497 0.2866976 0.4584956
[2,] 0.8589665 1.07934 1.57959 -0.5195754 -1.401497 0.2866976 0.4584956
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] 0.7055693 -1.134438 0.3883012 0.5505799 -1.529234 1.095672 -0.405931
[2,] 0.7055693 -1.134438 0.3883012 0.5505799 -1.529234 1.095672 -0.405931
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] 0.2532748 -0.2504702 1.177972 -0.5318916 -0.4301152 0.9125533 -1.705985
[2,] 0.2532748 -0.2504702 1.177972 -0.5318916 -0.4301152 0.9125533 -1.705985
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] 0.7698973 -0.7895711 -0.8040304 -0.1689227 0.2249644 -0.1871922 -1.126238
[2,] 0.7698973 -0.7895711 -0.8040304 -0.1689227 0.2249644 -0.1871922 -1.126238
[,64] [,65] [,66] [,67] [,68] [,69] [,70]
[1,] 0.8067895 0.1570701 0.6002449 0.5584598 1.262219 -1.646462 0.1200471
[2,] 0.8067895 0.1570701 0.6002449 0.5584598 1.262219 -1.646462 0.1200471
[,71] [,72] [,73] [,74] [,75] [,76] [,77] [,78]
[1,] 0.982482 0.6520215 1.441313 -1.3005 -2.292701 0.138834 0.2642669 0.7333703
[2,] 0.982482 0.6520215 1.441313 -1.3005 -2.292701 0.138834 0.2642669 0.7333703
[,79] [,80] [,81] [,82] [,83] [,84] [,85]
[1,] -0.01509166 -2.374874 -0.009218994 2.321952 0.6174608 -1.063588 -0.7024809
[2,] -0.01509166 -2.374874 -0.009218994 2.321952 0.6174608 -1.063588 -0.7024809
[,86] [,87] [,88] [,89] [,90] [,91] [,92]
[1,] -0.1085502 1.781461 1.201112 -0.7264834 -0.6033281 -0.4370277 -0.02330466
[2,] -0.1085502 1.781461 1.201112 -0.7264834 -0.6033281 -0.4370277 -0.02330466
[,93] [,94] [,95] [,96] [,97] [,98] [,99]
[1,] 0.3082821 0.9076194 -1.800698 1.3419 -0.8360673 -0.2681435 0.02285962
[2,] 0.3082821 0.9076194 -1.800698 1.3419 -0.8360673 -0.2681435 0.02285962
[,100]
[1,] -0.592766
[2,] -0.592766
>
>
> Max(tmp2)
[1] 2.238368
> Min(tmp2)
[1] -2.771329
> mean(tmp2)
[1] 0.1921313
> Sum(tmp2)
[1] 19.21313
> Var(tmp2)
[1] 1.108054
>
> rowMeans(tmp2)
[1] -1.83780304 0.87135109 1.12605184 0.18486031 0.08111970 0.64590239
[7] -0.46932032 -0.14553926 -1.14954586 1.55822070 1.22970712 1.29964459
[13] -1.06184018 1.70259031 0.21748151 0.21348258 -1.25816548 -0.01149147
[19] -0.01387469 -0.09404580 1.21434200 1.08894762 1.18519246 0.95270131
[25] 2.08301383 1.80005912 0.11797296 -0.17231903 0.58953601 0.31178878
[31] 0.51100295 0.30078680 1.15001390 -1.35287651 1.37619233 -1.98736829
[37] 0.17771518 1.59020749 1.52091560 -0.01098138 0.44202096 0.62653594
[43] -0.89655940 1.96541400 -0.28003498 1.95802142 -1.70393816 0.69715727
[49] -2.77132858 0.61891100 -1.57828387 -0.74778741 1.41859584 0.59830223
[55] -0.74062251 0.75723976 2.23836760 0.65344455 0.97326812 0.48669331
[61] 0.66633284 0.78422760 -0.49818836 0.91889291 -0.46109724 0.54924763
[67] -0.88321510 -0.22649157 0.06931831 -1.47686510 -0.25884352 0.10312924
[73] 1.03200398 0.58281346 -0.82790878 2.04738039 -0.29616655 1.03051222
[79] -0.36788184 -0.15824586 -0.30137439 -1.38653219 0.91327313 -0.42924111
[85] -0.78935742 -1.15577745 -1.21344496 -0.38369175 -0.22841734 -0.39481263
[91] 0.25865454 1.84216143 0.03524046 0.06497248 0.92193201 -0.96462176
[97] -1.47746031 -1.18691873 0.41115290 2.09739023
> rowSums(tmp2)
[1] -1.83780304 0.87135109 1.12605184 0.18486031 0.08111970 0.64590239
[7] -0.46932032 -0.14553926 -1.14954586 1.55822070 1.22970712 1.29964459
[13] -1.06184018 1.70259031 0.21748151 0.21348258 -1.25816548 -0.01149147
[19] -0.01387469 -0.09404580 1.21434200 1.08894762 1.18519246 0.95270131
[25] 2.08301383 1.80005912 0.11797296 -0.17231903 0.58953601 0.31178878
[31] 0.51100295 0.30078680 1.15001390 -1.35287651 1.37619233 -1.98736829
[37] 0.17771518 1.59020749 1.52091560 -0.01098138 0.44202096 0.62653594
[43] -0.89655940 1.96541400 -0.28003498 1.95802142 -1.70393816 0.69715727
[49] -2.77132858 0.61891100 -1.57828387 -0.74778741 1.41859584 0.59830223
[55] -0.74062251 0.75723976 2.23836760 0.65344455 0.97326812 0.48669331
[61] 0.66633284 0.78422760 -0.49818836 0.91889291 -0.46109724 0.54924763
[67] -0.88321510 -0.22649157 0.06931831 -1.47686510 -0.25884352 0.10312924
[73] 1.03200398 0.58281346 -0.82790878 2.04738039 -0.29616655 1.03051222
[79] -0.36788184 -0.15824586 -0.30137439 -1.38653219 0.91327313 -0.42924111
[85] -0.78935742 -1.15577745 -1.21344496 -0.38369175 -0.22841734 -0.39481263
[91] 0.25865454 1.84216143 0.03524046 0.06497248 0.92193201 -0.96462176
[97] -1.47746031 -1.18691873 0.41115290 2.09739023
> 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] -1.83780304 0.87135109 1.12605184 0.18486031 0.08111970 0.64590239
[7] -0.46932032 -0.14553926 -1.14954586 1.55822070 1.22970712 1.29964459
[13] -1.06184018 1.70259031 0.21748151 0.21348258 -1.25816548 -0.01149147
[19] -0.01387469 -0.09404580 1.21434200 1.08894762 1.18519246 0.95270131
[25] 2.08301383 1.80005912 0.11797296 -0.17231903 0.58953601 0.31178878
[31] 0.51100295 0.30078680 1.15001390 -1.35287651 1.37619233 -1.98736829
[37] 0.17771518 1.59020749 1.52091560 -0.01098138 0.44202096 0.62653594
[43] -0.89655940 1.96541400 -0.28003498 1.95802142 -1.70393816 0.69715727
[49] -2.77132858 0.61891100 -1.57828387 -0.74778741 1.41859584 0.59830223
[55] -0.74062251 0.75723976 2.23836760 0.65344455 0.97326812 0.48669331
[61] 0.66633284 0.78422760 -0.49818836 0.91889291 -0.46109724 0.54924763
[67] -0.88321510 -0.22649157 0.06931831 -1.47686510 -0.25884352 0.10312924
[73] 1.03200398 0.58281346 -0.82790878 2.04738039 -0.29616655 1.03051222
[79] -0.36788184 -0.15824586 -0.30137439 -1.38653219 0.91327313 -0.42924111
[85] -0.78935742 -1.15577745 -1.21344496 -0.38369175 -0.22841734 -0.39481263
[91] 0.25865454 1.84216143 0.03524046 0.06497248 0.92193201 -0.96462176
[97] -1.47746031 -1.18691873 0.41115290 2.09739023
> rowMin(tmp2)
[1] -1.83780304 0.87135109 1.12605184 0.18486031 0.08111970 0.64590239
[7] -0.46932032 -0.14553926 -1.14954586 1.55822070 1.22970712 1.29964459
[13] -1.06184018 1.70259031 0.21748151 0.21348258 -1.25816548 -0.01149147
[19] -0.01387469 -0.09404580 1.21434200 1.08894762 1.18519246 0.95270131
[25] 2.08301383 1.80005912 0.11797296 -0.17231903 0.58953601 0.31178878
[31] 0.51100295 0.30078680 1.15001390 -1.35287651 1.37619233 -1.98736829
[37] 0.17771518 1.59020749 1.52091560 -0.01098138 0.44202096 0.62653594
[43] -0.89655940 1.96541400 -0.28003498 1.95802142 -1.70393816 0.69715727
[49] -2.77132858 0.61891100 -1.57828387 -0.74778741 1.41859584 0.59830223
[55] -0.74062251 0.75723976 2.23836760 0.65344455 0.97326812 0.48669331
[61] 0.66633284 0.78422760 -0.49818836 0.91889291 -0.46109724 0.54924763
[67] -0.88321510 -0.22649157 0.06931831 -1.47686510 -0.25884352 0.10312924
[73] 1.03200398 0.58281346 -0.82790878 2.04738039 -0.29616655 1.03051222
[79] -0.36788184 -0.15824586 -0.30137439 -1.38653219 0.91327313 -0.42924111
[85] -0.78935742 -1.15577745 -1.21344496 -0.38369175 -0.22841734 -0.39481263
[91] 0.25865454 1.84216143 0.03524046 0.06497248 0.92193201 -0.96462176
[97] -1.47746031 -1.18691873 0.41115290 2.09739023
>
> colMeans(tmp2)
[1] 0.1921313
> colSums(tmp2)
[1] 19.21313
> colVars(tmp2)
[1] 1.108054
> colSd(tmp2)
[1] 1.052641
> colMax(tmp2)
[1] 2.238368
> colMin(tmp2)
[1] -2.771329
> colMedians(tmp2)
[1] 0.1991714
> colRanges(tmp2)
[,1]
[1,] -2.771329
[2,] 2.238368
>
> 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] -0.38715992 -0.15686874 -0.03982981 2.35838755 -0.80636269 -0.46636022
[7] 1.99053011 -2.35360911 -0.16903855 1.13005656
> colApply(tmp,quantile)[,1]
[,1]
[1,] -0.84509902
[2,] -0.26525116
[3,] -0.08595524
[4,] 0.40098901
[5,] 0.75224954
>
> rowApply(tmp,sum)
[1] 0.9794139 6.3192536 1.8718650 0.7261508 -1.1004006 -6.2092667
[7] -0.6007421 2.6796807 -2.9304837 -0.6357256
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 6 1 6 6 9 4 4 2 6 6
[2,] 2 4 8 7 10 8 2 3 8 1
[3,] 7 5 4 10 6 1 8 7 1 7
[4,] 9 6 9 9 1 3 6 6 3 8
[5,] 10 3 2 2 2 10 1 1 7 10
[6,] 4 2 3 5 7 2 5 9 9 5
[7,] 8 7 1 4 8 7 10 10 5 4
[8,] 5 10 5 1 5 5 9 5 2 2
[9,] 3 8 7 3 4 9 3 4 4 9
[10,] 1 9 10 8 3 6 7 8 10 3
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] 1.0599025 -0.5416105 2.9551738 -3.5098536 1.1576871 6.1698807
[7] -5.3284697 -2.2323767 -0.2459294 -0.8906864 -2.8445465 3.3137894
[13] 0.2820881 1.0676738 2.7433079 1.0245447 -3.2596833 0.3067358
[19] 2.6346119 2.2339195
> colApply(tmp,quantile)[,1]
[,1]
[1,] -0.43519642
[2,] -0.25132468
[3,] 0.09990544
[4,] 0.78473361
[5,] 0.86178457
>
> rowApply(tmp,sum)
[1] -3.748920 1.063018 6.345379 1.305600 1.131081
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 16 13 15 8 8
[2,] 14 15 10 3 9
[3,] 20 3 20 7 6
[4,] 2 10 4 5 5
[5,] 19 19 6 6 4
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 0.78473361 0.324354185 2.8194592 -1.68686711 1.0899837 1.0672177
[2,] 0.09990544 0.579034872 -0.9128609 -0.04903025 1.6767788 -0.2691046
[3,] 0.86178457 -0.002613424 2.1359528 -0.21936568 -0.1254804 0.9970275
[4,] -0.43519642 -1.224593577 -0.5200464 -0.96061607 -0.8149375 1.4575969
[5,] -0.25132468 -0.217792590 -0.5673309 -0.59397452 -0.6686574 2.9171432
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] -1.5542220 -0.4021798 -2.3912235 0.4007357 -1.12260000 -0.78159677
[2,] -1.2816292 -0.7910121 -0.7682709 -0.6541254 -0.95886291 1.74957718
[3,] -0.9968676 0.6790730 -0.9337852 -0.5871441 -0.05318371 1.46698897
[4,] -1.3230813 -1.0315913 1.7939137 0.7139932 0.99258874 0.86131224
[5,] -0.1726695 -0.6866664 2.0534365 -0.7641459 -1.70248865 0.01750778
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] -1.21279316 -0.6811273 0.24008875 -0.39628285 -0.6262557 -0.68420803
[2,] 1.33555138 0.8207734 0.05809189 -0.21186169 -0.8924595 1.30078120
[3,] 0.40759866 -0.1248628 0.99344122 0.74190105 -0.1109404 -0.12782865
[4,] 0.05710059 0.8779826 0.84087386 -0.04380934 -1.7454290 -0.01761223
[5,] -0.30536935 0.1749079 0.61081215 0.93459749 0.1154013 -0.16439653
[,19] [,20]
[1,] 1.02411090 0.03975273
[2,] 0.05886573 0.17287577
[3,] 0.35009725 0.99358661
[4,] 1.16823754 0.65891368
[5,] 0.03330052 0.36879067
>
>
> is.BufferedMatrix(tmp)
[1] TRUE
>
> as.BufferedMatrix(as.matrix(tmp))
BufferedMatrix object
Matrix size: 5 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.22-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: /home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 654 bytes.
Disk usage : 200 bytes.
> subBufferedMatrix(tmp,,5:8)
BufferedMatrix object
Matrix size: 5 4
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 565 bytes.
Disk usage : 160 bytes.
> subBufferedMatrix(tmp,1:3,)
BufferedMatrix object
Matrix size: 3 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.22-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 0.1538546 0.6637241 0.04989766 0.6080832 -0.8384087 1.097001 1.071549
col8 col9 col10 col11 col12 col13 col14
row1 -0.9800426 1.973422 -0.2080905 -0.1276292 -2.069097 -0.3804635 0.04919374
col15 col16 col17 col18 col19 col20
row1 -0.5582073 -0.8922653 0.756644 0.325366 -0.7005341 -0.526146
> tmp[,"col10"]
col10
row1 -0.2080905
row2 1.9583440
row3 -2.1249841
row4 -0.9152880
row5 0.1307031
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6
row1 0.1538546 0.66372414 0.04989766 0.6080832 -0.83840874 1.097001
row5 -0.2847185 -0.02814066 -0.30462469 0.4217574 0.09886416 -1.083263
col7 col8 col9 col10 col11 col12
row1 1.071549 -0.9800426 1.9734216 -0.2080905 -0.1276292 -2.06909692
row5 -0.529065 -0.5716625 -0.7897243 0.1307031 -1.2807878 -0.01920682
col13 col14 col15 col16 col17 col18
row1 -0.3804635 0.04919374 -0.5582073 -0.8922653 0.75664404 0.3253660
row5 0.5775191 -0.15450391 -0.2193094 0.1230437 0.04916828 -0.8224359
col19 col20
row1 -0.7005341 -0.5261460
row5 1.5211966 0.9755898
> tmp[,c("col6","col20")]
col6 col20
row1 1.0970012 -0.5261460
row2 0.6595849 -0.8803137
row3 0.9742947 -1.5013008
row4 1.1910951 1.4373841
row5 -1.0832625 0.9755898
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 1.097001 -0.5261460
row5 -1.083263 0.9755898
>
>
>
>
> 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 51.30839 48.46605 51.17083 49.83552 50.551 105.2205 50.85138 50.68565
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.64259 50.56219 50.59773 48.35105 51.03756 48.9293 51.38324 50.56353
col17 col18 col19 col20
row1 51.04344 49.54652 50.44325 105.3138
> tmp[,"col10"]
col10
row1 50.56219
row2 31.48248
row3 30.03153
row4 31.27300
row5 49.19870
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 51.30839 48.46605 51.17083 49.83552 50.55100 105.2205 50.85138 50.68565
row5 51.86496 50.75247 50.22010 51.36993 50.60642 105.0162 50.66497 50.96288
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.64259 50.56219 50.59773 48.35105 51.03756 48.92930 51.38324 50.56353
row5 51.22197 49.19870 51.60475 49.40038 50.70188 49.10874 49.69175 50.70732
col17 col18 col19 col20
row1 51.04344 49.54652 50.44325 105.3138
row5 51.30844 49.16897 48.93893 104.5354
> tmp[,c("col6","col20")]
col6 col20
row1 105.22048 105.31376
row2 75.40804 74.07699
row3 74.68847 75.13714
row4 74.44865 75.13500
row5 105.01619 104.53541
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 105.2205 105.3138
row5 105.0162 104.5354
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 105.2205 105.3138
row5 105.0162 104.5354
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] 1.9240411
[2,] -1.0509652
[3,] 1.3896430
[4,] 1.1003549
[5,] 0.2638223
> tmp[,c("col17","col7")]
col17 col7
[1,] 1.1205105 -0.8402770
[2,] -0.6702770 0.9387972
[3,] -0.8070007 -1.8015912
[4,] -0.5619066 -0.4357997
[5,] 0.2560137 2.0144120
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] 0.7331367 0.1240415
[2,] -0.5213857 0.3070194
[3,] 0.6345120 1.3308567
[4,] -1.1025941 0.5861380
[5,] -0.4450331 -0.6326132
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] 0.7331367
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] 0.7331367
[2,] -0.5213857
>
>
>
> 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 0.3344128 0.7642340 0.9270942 0.2900849 0.4364125 -0.1572117 -0.02424175
row1 0.8785511 0.5038041 -0.4636167 -0.2502032 0.4248308 -0.5920821 0.55129937
[,8] [,9] [,10] [,11] [,12] [,13]
row3 0.1844822 -0.9807811 -0.2968712 -0.04303987 -1.5549157 -0.689219
row1 0.3166577 2.2494378 -0.5523391 1.13903944 0.4714729 1.101346
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
row3 -1.1534114 0.7107453 -3.120343 0.5914327 -1.1766392 0.8453900 -0.6782336
row1 -0.2292919 -1.0056848 -0.124943 1.4284574 0.1499747 -0.4037506 0.2554339
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 0.1613204 -1.022116 -0.6286366 0.1200308 0.4499774 -1.788752 -1.239425
[,8] [,9] [,10]
row2 -0.2738917 0.06195044 -0.8251617
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 0.00500288 -2.364159 -0.1644791 0.6246597 1.116751 0.8896319 0.4802917
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 -0.1497351 0.3558847 1.165988 -0.4147861 -0.6355502 0.5417907 -0.6722696
[,15] [,16] [,17] [,18] [,19] [,20]
row5 -0.838789 -0.2411983 0.07463863 0.3103274 0.7580904 -0.3054571
>
>
> 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: 0xeef69e0>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2232d153e90233"
[2] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2232d165d9c3a6"
[3] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2232d11ec3e0"
[4] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2232d17e0dfba5"
[5] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2232d17d574ca2"
[6] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2232d193a2f63"
[7] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2232d161115992"
[8] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2232d14480d57d"
[9] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2232d14a5950fa"
[10] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2232d1554df371"
[11] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2232d12ea11b70"
[12] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2232d14aa979ae"
[13] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2232d11e4d2e0"
[14] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2232d13c59fe88"
[15] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2232d1548b3462"
>
>
> ### 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: 0xe95aa90>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0xe95aa90>
Warning message:
In dir.create(new.directory) :
'/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0xe95aa90>
> rowMedians(tmp)
[1] 0.166252610 -0.385228586 0.184926290 0.217262197 0.051406655
[6] 0.365469760 -0.104646224 0.114672190 -0.356015710 -0.047164766
[11] -0.245243395 -0.191922128 0.557463276 0.276971901 0.166688651
[16] 0.121015095 0.584252130 -0.217452827 -0.279348357 -0.010673369
[21] -0.192052643 0.838198808 0.180816346 0.070551728 0.473486786
[26] 0.285695341 -0.251211328 -0.344472946 -0.439306581 -0.300369883
[31] 0.479876872 -0.123133376 -0.315058031 0.617558352 -0.390288423
[36] -0.413617095 0.135372940 -0.359235891 0.226487480 -0.162527089
[41] 0.454690488 0.441487371 0.082175259 0.030790974 -0.011110426
[46] -0.041195747 0.358383004 -0.089410288 -0.156385653 0.259305485
[51] -0.182104969 0.123921947 0.201731143 0.173741689 0.421797799
[56] -0.386614472 -0.110868350 -0.015240143 0.226569777 0.043587219
[61] -0.321035915 0.242398353 -0.060650522 0.517303745 0.356550652
[66] -0.242017261 -0.172401706 -0.017649298 -0.009564372 -0.126165005
[71] -0.472414296 0.158037368 0.162824000 -0.324846941 -0.051785310
[76] -0.288886191 0.144776310 -0.246368442 -0.512162297 -0.015272208
[81] 0.107399564 0.003365034 -0.115954976 0.320943370 0.217463728
[86] -0.051838610 -0.034739400 0.142504391 -0.072888468 -0.211991607
[91] -0.178862610 0.260274986 -0.043874482 -0.425040373 0.242043773
[96] -0.090187342 0.129335077 -0.446184533 -0.080701189 0.650274615
[101] -0.389446803 0.431922992 -0.396907985 0.254167507 0.432636687
[106] -0.027532066 0.211059977 0.443758181 -0.475517610 0.016641124
[111] -0.323158621 0.206686746 0.560254850 0.195429482 -0.079306276
[116] 0.051481910 0.229643517 -0.520510035 0.121997384 -0.177783099
[121] 0.508536568 -0.378367719 -0.389117042 -0.078929943 0.759255027
[126] -0.208422610 0.413904901 0.003388959 0.796893868 -0.588916869
[131] 0.027575713 0.466182691 -0.513492819 -0.736012948 0.071871900
[136] -0.285277570 -0.240143691 -0.099409797 0.316586300 0.064109144
[141] -0.062733580 -0.319265286 0.355452434 -0.370883056 0.506873371
[146] -0.425952103 0.345383865 0.412935430 0.341076561 -0.124564726
[151] 0.126932811 0.236168324 -0.263265980 -0.598825932 0.057640131
[156] 0.241437432 -0.099650659 0.036934760 -0.035043383 0.098705121
[161] 0.696760754 0.050599707 -0.143796734 0.100609556 -0.340236921
[166] -0.035994421 -0.120046926 -0.452874452 -0.059038817 0.490319381
[171] 0.063139963 -0.042037964 0.681568680 0.389627065 -0.188715253
[176] -0.631601224 -0.399526657 0.132611298 0.031965905 0.147652661
[181] 0.386481451 -0.033937348 -0.836236052 -0.422979311 0.015022547
[186] -0.110964927 -0.018735765 0.624565724 -0.298750751 0.058642347
[191] 0.420375709 -0.273462326 0.525356045 0.420690214 0.315775001
[196] -0.332892504 -0.653878223 0.243781314 -0.245060418 0.298880501
[201] -0.297750371 -0.490720186 0.668095892 0.408515414 0.574506509
[206] -0.251268600 -0.170270267 0.343630227 -0.055693724 -0.130459351
[211] 0.323468883 0.108768481 -0.382356941 -0.100012897 0.055806663
[216] -0.177351541 0.238139072 -0.124409557 0.266085580 -0.077760279
[221] 0.452102033 -0.662325626 0.420464959 0.213371452 -0.036339062
[226] 0.291975660 -0.390352483 0.253247206 -0.768866431 -0.249058006
>
> proc.time()
user system elapsed
1.977 0.839 2.841
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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: 0x3ffa0ff0>
> .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: 0x3ffa0ff0>
> .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: 0x3ffa0ff0>
> .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: 0x3ffa0ff0>
> 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: 0x3fe860e0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x3fe860e0>
> .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: 0x3fe860e0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x3fe860e0>
> .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: 0x3fe860e0>
> 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: 0x3ee0d520>
> .Call("R_bm_AddColumn",P)
<pointer: 0x3ee0d520>
> .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: 0x3ee0d520>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x3ee0d520>
> .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: 0x3ee0d520>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x3ee0d520>
> .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: 0x3ee0d520>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x3ee0d520>
> .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: 0x3ee0d520>
> 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: 0x3e811720>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x3e811720>
> .Call("R_bm_AddColumn",P)
<pointer: 0x3e811720>
> .Call("R_bm_AddColumn",P)
<pointer: 0x3e811720>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile22332538dad415" "BufferedMatrixFile223325c963028"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile22332538dad415" "BufferedMatrixFile223325c963028"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x3f7017d0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x3f7017d0>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x3f7017d0>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x3f7017d0>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x3f7017d0>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x3f7017d0>
> .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: 0x3f808c90>
> .Call("R_bm_AddColumn",P)
<pointer: 0x3f808c90>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x3f808c90>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x3f808c90>
> 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: 0x40ab1110>
> .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: 0x40ab1110>
> rm(P)
>
> proc.time()
user system elapsed
0.336 0.038 0.359
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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
0.312 0.055 0.352