Ben Bolstad
| Snapshot Date: 2026-02-05 13:45 -0500 (Thu, 05 Feb 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 Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-02-09 11:57 -0500 (Mon, 09 Feb 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" | 4888 |
| 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 | | ||||||||
| See other builds for BufferedMatrix in R Universe. | ||||||||||||||
|
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: 1.74.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BufferedMatrix_1.74.0.tar.gz |
| StartedAt: 2026-02-05 21:43:47 -0500 (Thu, 05 Feb 2026) |
| EndedAt: 2026-02-05 21:44:11 -0500 (Thu, 05 Feb 2026) |
| EllapsedTime: 24.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BufferedMatrix.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BufferedMatrix_1.74.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 re-building of vignette outputs ... OK
* 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
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###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL BufferedMatrix
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘BufferedMatrix’ ...
** this is package ‘BufferedMatrix’ version ‘1.74.0’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RBufferedMatrix.c -o RBufferedMatrix.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/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){
| ^~~~~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c doubleBufferedMatrix_C_tests.c -o doubleBufferedMatrix_C_tests.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c init_package.c -o init_package.o
gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o BufferedMatrix.so RBufferedMatrix.o doubleBufferedMatrix.o doubleBufferedMatrix_C_tests.o init_package.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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
0.250 0.041 0.280
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 478284 25.6 1046725 56 639600 34.2
Vcells 884773 6.8 8388608 64 2081613 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] "Thu Feb 5 21:44:02 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] "Thu Feb 5 21:44:03 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: 0x628a50b4d1c0>
>
>
>
> 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] "Thu Feb 5 21:44:03 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] "Thu Feb 5 21:44:03 2026"
>
> ColMode(tmp2)
<pointer: 0x628a50b4d1c0>
>
>
>
> ### Now testing assignments
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+
+ new.data <- rnorm(20)
+ tmp2[which.row,] <- new.data
+ test.matrix[which.row,] <- new.data
+ if (rep > 1){
+ if (!all(tmp2[prev.row,] == test.matrix[prev.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ new.data <- rnorm(10)
+ tmp2[,which.col] <- new.data
+ test.matrix[,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[,prev.col] == test.matrix[,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.col <- which.col
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,5,replace=TRUE)
+ new.data <- matrix(rnorm(50),5,10)
+ tmp2[,which.col] <- new.data
+ test.matrix[,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[,prev.col] == test.matrix[,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.col <- which.col
+ }
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ new.data <- matrix(rnorm(50),5,10)
+ tmp2[which.row,] <- new.data
+ test.matrix[which.row,]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[prev.row,] == test.matrix[prev.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:20,5,replace=TRUE)
+ new.data <- matrix(rnorm(25),5,5)
+ tmp2[which.row,which.col] <- new.data
+ test.matrix[which.row,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[prev.row,prev.col] == test.matrix[prev.row,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+ prev.col <- which.col
+ }
>
>
>
>
> ###
> ###
> ### testing some more functions
> ###
>
>
>
> ## duplication function
> tmp5 <- duplicate(tmp2)
>
> # making sure really did copy everything.
> tmp5[1,1] <- tmp5[1,1] +100.00
>
> if (tmp5[1,1] == tmp2[1,1]){
+ stop("Problem with duplication")
+ }
>
>
>
>
> ### testing elementwise applying of functions
>
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 99.084741834 1.04921121 0.1055990 0.3296700
[2,] 0.334903375 0.73464140 -2.0864313 0.6394418
[3,] 0.002193006 0.05891797 -0.2294185 0.4438803
[4,] 1.107644083 -0.27815475 -0.5059408 0.9786523
> 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 : 1.9 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 99.084741834 1.04921121 0.1055990 0.3296700
[2,] 0.334903375 0.73464140 2.0864313 0.6394418
[3,] 0.002193006 0.05891797 0.2294185 0.4438803
[4,] 1.107644083 0.27815475 0.5059408 0.9786523
> 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 : 1.9 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 9.95413190 1.0243101 0.3249600 0.5741689
[2,] 0.57870837 0.8571122 1.4444484 0.7996511
[3,] 0.04682955 0.2427303 0.4789766 0.6662434
[4,] 1.05244671 0.5274038 0.7112951 0.9892686
>
> 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 : 1.9 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 223.62606 36.29231 28.35520 31.07136
[2,] 31.12199 34.30576 41.53092 33.63595
[3,] 25.47049 27.48622 30.01918 32.10631
[4,] 36.63211 30.55219 32.61889 35.87134
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x628a517538b0>
> exp(tmp5)
<pointer: 0x628a517538b0>
> log(tmp5,2)
<pointer: 0x628a517538b0>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 465.4483
> Min(tmp5)
[1] 53.01348
> mean(tmp5)
[1] 72.28434
> Sum(tmp5)
[1] 14456.87
> Var(tmp5)
[1] 850.3787
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 92.96531 69.00872 69.39493 72.50934 69.43586 70.02924 69.92723 69.32408
[9] 71.50350 68.74513
> rowSums(tmp5)
[1] 1859.306 1380.174 1387.899 1450.187 1388.717 1400.585 1398.545 1386.482
[9] 1430.070 1374.903
> rowVars(tmp5)
[1] 7767.46698 66.18798 90.45667 43.49259 91.00044 43.06220
[7] 73.38307 55.83957 83.32960 79.23619
> rowSd(tmp5)
[1] 88.133234 8.135599 9.510871 6.594891 9.539415 6.562180 8.566392
[8] 7.472588 9.128505 8.901471
> rowMax(tmp5)
[1] 465.44835 86.44116 88.14554 81.01527 96.08273 81.66024 89.42229
[8] 85.65383 88.03443 85.73811
> rowMin(tmp5)
[1] 59.01763 57.50614 53.01348 54.04349 56.79626 57.53659 54.01496 55.70551
[9] 55.32080 55.49347
>
> colMeans(tmp5)
[1] 108.10259 67.79511 70.04696 69.02799 72.13787 69.89599 71.42936
[8] 69.40979 70.64973 68.54593 76.17379 72.99582 70.20359 68.82052
[15] 71.14157 71.15167 70.81649 74.89336 66.00652 66.44207
> colSums(tmp5)
[1] 1081.0259 677.9511 700.4696 690.2799 721.3787 698.9599 714.2936
[8] 694.0979 706.4973 685.4593 761.7379 729.9582 702.0359 688.2052
[15] 711.4157 711.5167 708.1649 748.9336 660.0652 664.4207
> colVars(tmp5)
[1] 15835.12875 38.13422 153.82902 35.94199 56.56239 32.18841
[7] 177.17255 45.95590 37.89681 60.10846 76.97472 61.35086
[13] 51.00463 38.11250 52.63529 89.76351 60.61774 119.98014
[19] 33.45944 115.85400
> colSd(tmp5)
[1] 125.837708 6.175291 12.402783 5.995163 7.520797 5.673483
[7] 13.310618 6.779078 6.156039 7.752965 8.773524 7.832679
[13] 7.141753 6.173532 7.255019 9.474361 7.785739 10.953545
[19] 5.784414 10.763549
> colMax(tmp5)
[1] 465.44835 75.53769 88.03443 74.84418 83.09904 78.68070 89.42229
[8] 78.23676 81.49880 81.45737 97.21223 85.49455 82.17661 79.13978
[15] 82.08819 88.14554 86.38259 96.08273 78.72422 84.76391
> colMin(tmp5)
[1] 53.01348 57.20897 57.72165 55.32080 60.81424 60.15981 54.04349 58.75661
[9] 60.79601 57.86060 63.63143 64.37084 63.10588 56.69212 59.95891 61.92778
[17] 58.76048 57.50614 58.59126 54.01496
>
>
> ### setting a random element to NA and then testing with na.rm=TRUE or na.rm=FALSE (The default)
>
>
> which.row <- sample(1:10,1,replace=TRUE)
> which.col <- sample(1:20,1,replace=TRUE)
>
> tmp5[which.row,which.col] <- NA
>
> Max(tmp5)
[1] NA
> Min(tmp5)
[1] NA
> mean(tmp5)
[1] NA
> Sum(tmp5)
[1] NA
> Var(tmp5)
[1] NA
>
> rowMeans(tmp5)
[1] 92.96531 69.00872 69.39493 72.50934 69.43586 70.02924 69.92723 69.32408
[9] 71.50350 NA
> rowSums(tmp5)
[1] 1859.306 1380.174 1387.899 1450.187 1388.717 1400.585 1398.545 1386.482
[9] 1430.070 NA
> rowVars(tmp5)
[1] 7767.46698 66.18798 90.45667 43.49259 91.00044 43.06220
[7] 73.38307 55.83957 83.32960 80.97018
> rowSd(tmp5)
[1] 88.133234 8.135599 9.510871 6.594891 9.539415 6.562180 8.566392
[8] 7.472588 9.128505 8.998343
> rowMax(tmp5)
[1] 465.44835 86.44116 88.14554 81.01527 96.08273 81.66024 89.42229
[8] 85.65383 88.03443 NA
> rowMin(tmp5)
[1] 59.01763 57.50614 53.01348 54.04349 56.79626 57.53659 54.01496 55.70551
[9] 55.32080 NA
>
> colMeans(tmp5)
[1] 108.10259 67.79511 70.04696 69.02799 72.13787 NA 71.42936
[8] 69.40979 70.64973 68.54593 76.17379 72.99582 70.20359 68.82052
[15] 71.14157 71.15167 70.81649 74.89336 66.00652 66.44207
> colSums(tmp5)
[1] 1081.0259 677.9511 700.4696 690.2799 721.3787 NA 714.2936
[8] 694.0979 706.4973 685.4593 761.7379 729.9582 702.0359 688.2052
[15] 711.4157 711.5167 708.1649 748.9336 660.0652 664.4207
> colVars(tmp5)
[1] 15835.12875 38.13422 153.82902 35.94199 56.56239 NA
[7] 177.17255 45.95590 37.89681 60.10846 76.97472 61.35086
[13] 51.00463 38.11250 52.63529 89.76351 60.61774 119.98014
[19] 33.45944 115.85400
> colSd(tmp5)
[1] 125.837708 6.175291 12.402783 5.995163 7.520797 NA
[7] 13.310618 6.779078 6.156039 7.752965 8.773524 7.832679
[13] 7.141753 6.173532 7.255019 9.474361 7.785739 10.953545
[19] 5.784414 10.763549
> colMax(tmp5)
[1] 465.44835 75.53769 88.03443 74.84418 83.09904 NA 89.42229
[8] 78.23676 81.49880 81.45737 97.21223 85.49455 82.17661 79.13978
[15] 82.08819 88.14554 86.38259 96.08273 78.72422 84.76391
> colMin(tmp5)
[1] 53.01348 57.20897 57.72165 55.32080 60.81424 NA 54.04349 58.75661
[9] 60.79601 57.86060 63.63143 64.37084 63.10588 56.69212 59.95891 61.92778
[17] 58.76048 57.50614 58.59126 54.01496
>
> Max(tmp5,na.rm=TRUE)
[1] 465.4483
> Min(tmp5,na.rm=TRUE)
[1] 53.01348
> mean(tmp5,na.rm=TRUE)
[1] 72.33606
> Sum(tmp5,na.rm=TRUE)
[1] 14394.88
> Var(tmp5,na.rm=TRUE)
[1] 854.1357
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 92.96531 69.00872 69.39493 72.50934 69.43586 70.02924 69.92723 69.32408
[9] 71.50350 69.10063
> rowSums(tmp5,na.rm=TRUE)
[1] 1859.306 1380.174 1387.899 1450.187 1388.717 1400.585 1398.545 1386.482
[9] 1430.070 1312.912
> rowVars(tmp5,na.rm=TRUE)
[1] 7767.46698 66.18798 90.45667 43.49259 91.00044 43.06220
[7] 73.38307 55.83957 83.32960 80.97018
> rowSd(tmp5,na.rm=TRUE)
[1] 88.133234 8.135599 9.510871 6.594891 9.539415 6.562180 8.566392
[8] 7.472588 9.128505 8.998343
> rowMax(tmp5,na.rm=TRUE)
[1] 465.44835 86.44116 88.14554 81.01527 96.08273 81.66024 89.42229
[8] 85.65383 88.03443 85.73811
> rowMin(tmp5,na.rm=TRUE)
[1] 59.01763 57.50614 53.01348 54.04349 56.79626 57.53659 54.01496 55.70551
[9] 55.32080 55.49347
>
> colMeans(tmp5,na.rm=TRUE)
[1] 108.10259 67.79511 70.04696 69.02799 72.13787 70.77436 71.42936
[8] 69.40979 70.64973 68.54593 76.17379 72.99582 70.20359 68.82052
[15] 71.14157 71.15167 70.81649 74.89336 66.00652 66.44207
> colSums(tmp5,na.rm=TRUE)
[1] 1081.0259 677.9511 700.4696 690.2799 721.3787 636.9692 714.2936
[8] 694.0979 706.4973 685.4593 761.7379 729.9582 702.0359 688.2052
[15] 711.4157 711.5167 708.1649 748.9336 660.0652 664.4207
> colVars(tmp5,na.rm=TRUE)
[1] 15835.12875 38.13422 153.82902 35.94199 56.56239 27.53217
[7] 177.17255 45.95590 37.89681 60.10846 76.97472 61.35086
[13] 51.00463 38.11250 52.63529 89.76351 60.61774 119.98014
[19] 33.45944 115.85400
> colSd(tmp5,na.rm=TRUE)
[1] 125.837708 6.175291 12.402783 5.995163 7.520797 5.247111
[7] 13.310618 6.779078 6.156039 7.752965 8.773524 7.832679
[13] 7.141753 6.173532 7.255019 9.474361 7.785739 10.953545
[19] 5.784414 10.763549
> colMax(tmp5,na.rm=TRUE)
[1] 465.44835 75.53769 88.03443 74.84418 83.09904 78.68070 89.42229
[8] 78.23676 81.49880 81.45737 97.21223 85.49455 82.17661 79.13978
[15] 82.08819 88.14554 86.38259 96.08273 78.72422 84.76391
> colMin(tmp5,na.rm=TRUE)
[1] 53.01348 57.20897 57.72165 55.32080 60.81424 60.15981 54.04349 58.75661
[9] 60.79601 57.86060 63.63143 64.37084 63.10588 56.69212 59.95891 61.92778
[17] 58.76048 57.50614 58.59126 54.01496
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 92.96531 69.00872 69.39493 72.50934 69.43586 70.02924 69.92723 69.32408
[9] 71.50350 NaN
> rowSums(tmp5,na.rm=TRUE)
[1] 1859.306 1380.174 1387.899 1450.187 1388.717 1400.585 1398.545 1386.482
[9] 1430.070 0.000
> rowVars(tmp5,na.rm=TRUE)
[1] 7767.46698 66.18798 90.45667 43.49259 91.00044 43.06220
[7] 73.38307 55.83957 83.32960 NA
> rowSd(tmp5,na.rm=TRUE)
[1] 88.133234 8.135599 9.510871 6.594891 9.539415 6.562180 8.566392
[8] 7.472588 9.128505 NA
> rowMax(tmp5,na.rm=TRUE)
[1] 465.44835 86.44116 88.14554 81.01527 96.08273 81.66024 89.42229
[8] 85.65383 88.03443 NA
> rowMin(tmp5,na.rm=TRUE)
[1] 59.01763 57.50614 53.01348 54.04349 56.79626 57.53659 54.01496 55.70551
[9] 55.32080 NA
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 111.19971 67.86490 71.41643 68.97349 72.17118 NaN 71.15421
[8] 68.55182 70.22857 69.50961 76.68316 73.95415 70.97521 70.16812
[15] 69.92528 69.53096 72.15605 74.86986 65.78596 67.65859
> colSums(tmp5,na.rm=TRUE)
[1] 1000.7974 610.7841 642.7479 620.7614 649.5406 0.0000 640.3879
[8] 616.9664 632.0572 625.5865 690.1485 665.5873 638.7769 631.5131
[15] 629.3275 625.7786 649.4044 673.8288 592.0736 608.9273
> colVars(tmp5,na.rm=TRUE)
[1] 17706.60814 42.84620 151.95861 40.40132 63.62020 NA
[7] 198.46738 43.41913 40.63848 57.17441 83.67766 58.68775
[13] 50.68186 22.44626 42.57186 71.43339 48.00782 134.97145
[19] 37.09461 113.68686
> colSd(tmp5,na.rm=TRUE)
[1] 133.066180 6.545701 12.327149 6.356203 7.976227 NA
[7] 14.087845 6.589319 6.374832 7.561376 9.147550 7.660793
[13] 7.119119 4.737748 6.524712 8.451827 6.928767 11.617721
[19] 6.090535 10.662404
> colMax(tmp5,na.rm=TRUE)
[1] 465.44835 75.53769 88.03443 74.84418 83.09904 -Inf 89.42229
[8] 78.23676 81.49880 81.45737 97.21223 85.49455 82.17661 79.13978
[15] 78.96636 88.14554 86.38259 96.08273 78.72422 84.76391
> colMin(tmp5,na.rm=TRUE)
[1] 53.01348 57.20897 59.01763 55.32080 60.81424 Inf 54.04349 58.75661
[9] 60.79601 57.86060 63.63143 65.00872 63.10588 63.74599 59.95891 61.92778
[17] 64.96333 57.50614 58.59126 54.01496
>
>
>
>
> 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] 220.5217 146.3332 263.9776 161.5177 216.0083 138.3884 302.3777 183.7044
[9] 262.1963 167.8756
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 220.5217 146.3332 263.9776 161.5177 216.0083 138.3884 302.3777 183.7044
[9] 262.1963 167.8756
>
>
>
> 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] -8.526513e-14 2.273737e-13 5.684342e-14 -2.842171e-13 5.684342e-14
[6] -1.705303e-13 0.000000e+00 -1.136868e-13 8.526513e-14 8.526513e-14
[11] -1.705303e-13 2.842171e-14 2.842171e-14 1.421085e-14 1.705303e-13
[16] -1.136868e-13 -2.557954e-13 1.136868e-13 -8.526513e-14 -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 6
6 1
2 1
2 3
9 17
3 10
10 14
9 12
5 18
2 15
7 11
9 19
7 9
5 13
10 14
6 6
2 18
6 11
10 18
2 15
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] 2.172002
> Min(tmp)
[1] -2.140596
> mean(tmp)
[1] -0.1663761
> Sum(tmp)
[1] -16.63761
> Var(tmp)
[1] 0.8955831
>
> rowMeans(tmp)
[1] -0.1663761
> rowSums(tmp)
[1] -16.63761
> rowVars(tmp)
[1] 0.8955831
> rowSd(tmp)
[1] 0.9463525
> rowMax(tmp)
[1] 2.172002
> rowMin(tmp)
[1] -2.140596
>
> colMeans(tmp)
[1] 0.060650595 1.271292157 0.679436104 -1.225648872 1.338044830
[6] -0.916161078 1.568303232 0.643466629 -1.800964264 -0.196096230
[11] -0.478142290 1.493578012 -0.976723910 -0.253413662 -0.024609251
[16] 0.333934410 -0.157233195 0.008671321 -0.358453902 0.967937483
[21] -1.623180226 0.492183852 0.155697123 -0.861605076 -1.008441546
[26] 1.905168098 1.393183005 -0.745812722 1.006439714 0.114991205
[31] 2.172002014 -0.751913473 0.180721615 -0.955966216 -0.053277930
[36] -0.361205767 -1.659353116 -0.576491993 -0.077583146 -0.581388196
[41] -0.537379128 -0.597168775 -0.548439986 -0.039147034 -1.169091364
[46] 2.137454024 0.821786477 0.239238798 -0.002546057 -0.069754554
[51] -0.569073102 -0.537882774 -0.399935908 -0.954161489 -1.048505676
[56] 0.420924922 -0.934108755 -0.973720790 -1.743805839 -0.931596305
[61] -1.939373629 -0.811586391 -0.566087775 1.076834851 0.765556339
[66] 1.567655274 0.162180643 -0.180988275 1.472835439 0.787518121
[71] 0.941836751 0.000571892 0.907848711 0.341258987 1.270600646
[76] -0.648134786 -0.833374007 -0.804929848 -0.048313370 -0.419910646
[81] -0.571045815 -0.108912474 1.535316801 -0.148706057 -1.348683009
[86] -0.321913951 -0.443173589 -0.210393202 -1.434157670 0.186697111
[91] -0.939197297 -0.942039175 -0.706436207 -0.666586761 -0.279622579
[96] -1.521853885 -2.140595760 -1.452463238 -0.170935487 -0.700030211
> colSums(tmp)
[1] 0.060650595 1.271292157 0.679436104 -1.225648872 1.338044830
[6] -0.916161078 1.568303232 0.643466629 -1.800964264 -0.196096230
[11] -0.478142290 1.493578012 -0.976723910 -0.253413662 -0.024609251
[16] 0.333934410 -0.157233195 0.008671321 -0.358453902 0.967937483
[21] -1.623180226 0.492183852 0.155697123 -0.861605076 -1.008441546
[26] 1.905168098 1.393183005 -0.745812722 1.006439714 0.114991205
[31] 2.172002014 -0.751913473 0.180721615 -0.955966216 -0.053277930
[36] -0.361205767 -1.659353116 -0.576491993 -0.077583146 -0.581388196
[41] -0.537379128 -0.597168775 -0.548439986 -0.039147034 -1.169091364
[46] 2.137454024 0.821786477 0.239238798 -0.002546057 -0.069754554
[51] -0.569073102 -0.537882774 -0.399935908 -0.954161489 -1.048505676
[56] 0.420924922 -0.934108755 -0.973720790 -1.743805839 -0.931596305
[61] -1.939373629 -0.811586391 -0.566087775 1.076834851 0.765556339
[66] 1.567655274 0.162180643 -0.180988275 1.472835439 0.787518121
[71] 0.941836751 0.000571892 0.907848711 0.341258987 1.270600646
[76] -0.648134786 -0.833374007 -0.804929848 -0.048313370 -0.419910646
[81] -0.571045815 -0.108912474 1.535316801 -0.148706057 -1.348683009
[86] -0.321913951 -0.443173589 -0.210393202 -1.434157670 0.186697111
[91] -0.939197297 -0.942039175 -0.706436207 -0.666586761 -0.279622579
[96] -1.521853885 -2.140595760 -1.452463238 -0.170935487 -0.700030211
> 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] 0.060650595 1.271292157 0.679436104 -1.225648872 1.338044830
[6] -0.916161078 1.568303232 0.643466629 -1.800964264 -0.196096230
[11] -0.478142290 1.493578012 -0.976723910 -0.253413662 -0.024609251
[16] 0.333934410 -0.157233195 0.008671321 -0.358453902 0.967937483
[21] -1.623180226 0.492183852 0.155697123 -0.861605076 -1.008441546
[26] 1.905168098 1.393183005 -0.745812722 1.006439714 0.114991205
[31] 2.172002014 -0.751913473 0.180721615 -0.955966216 -0.053277930
[36] -0.361205767 -1.659353116 -0.576491993 -0.077583146 -0.581388196
[41] -0.537379128 -0.597168775 -0.548439986 -0.039147034 -1.169091364
[46] 2.137454024 0.821786477 0.239238798 -0.002546057 -0.069754554
[51] -0.569073102 -0.537882774 -0.399935908 -0.954161489 -1.048505676
[56] 0.420924922 -0.934108755 -0.973720790 -1.743805839 -0.931596305
[61] -1.939373629 -0.811586391 -0.566087775 1.076834851 0.765556339
[66] 1.567655274 0.162180643 -0.180988275 1.472835439 0.787518121
[71] 0.941836751 0.000571892 0.907848711 0.341258987 1.270600646
[76] -0.648134786 -0.833374007 -0.804929848 -0.048313370 -0.419910646
[81] -0.571045815 -0.108912474 1.535316801 -0.148706057 -1.348683009
[86] -0.321913951 -0.443173589 -0.210393202 -1.434157670 0.186697111
[91] -0.939197297 -0.942039175 -0.706436207 -0.666586761 -0.279622579
[96] -1.521853885 -2.140595760 -1.452463238 -0.170935487 -0.700030211
> colMin(tmp)
[1] 0.060650595 1.271292157 0.679436104 -1.225648872 1.338044830
[6] -0.916161078 1.568303232 0.643466629 -1.800964264 -0.196096230
[11] -0.478142290 1.493578012 -0.976723910 -0.253413662 -0.024609251
[16] 0.333934410 -0.157233195 0.008671321 -0.358453902 0.967937483
[21] -1.623180226 0.492183852 0.155697123 -0.861605076 -1.008441546
[26] 1.905168098 1.393183005 -0.745812722 1.006439714 0.114991205
[31] 2.172002014 -0.751913473 0.180721615 -0.955966216 -0.053277930
[36] -0.361205767 -1.659353116 -0.576491993 -0.077583146 -0.581388196
[41] -0.537379128 -0.597168775 -0.548439986 -0.039147034 -1.169091364
[46] 2.137454024 0.821786477 0.239238798 -0.002546057 -0.069754554
[51] -0.569073102 -0.537882774 -0.399935908 -0.954161489 -1.048505676
[56] 0.420924922 -0.934108755 -0.973720790 -1.743805839 -0.931596305
[61] -1.939373629 -0.811586391 -0.566087775 1.076834851 0.765556339
[66] 1.567655274 0.162180643 -0.180988275 1.472835439 0.787518121
[71] 0.941836751 0.000571892 0.907848711 0.341258987 1.270600646
[76] -0.648134786 -0.833374007 -0.804929848 -0.048313370 -0.419910646
[81] -0.571045815 -0.108912474 1.535316801 -0.148706057 -1.348683009
[86] -0.321913951 -0.443173589 -0.210393202 -1.434157670 0.186697111
[91] -0.939197297 -0.942039175 -0.706436207 -0.666586761 -0.279622579
[96] -1.521853885 -2.140595760 -1.452463238 -0.170935487 -0.700030211
> colMedians(tmp)
[1] 0.060650595 1.271292157 0.679436104 -1.225648872 1.338044830
[6] -0.916161078 1.568303232 0.643466629 -1.800964264 -0.196096230
[11] -0.478142290 1.493578012 -0.976723910 -0.253413662 -0.024609251
[16] 0.333934410 -0.157233195 0.008671321 -0.358453902 0.967937483
[21] -1.623180226 0.492183852 0.155697123 -0.861605076 -1.008441546
[26] 1.905168098 1.393183005 -0.745812722 1.006439714 0.114991205
[31] 2.172002014 -0.751913473 0.180721615 -0.955966216 -0.053277930
[36] -0.361205767 -1.659353116 -0.576491993 -0.077583146 -0.581388196
[41] -0.537379128 -0.597168775 -0.548439986 -0.039147034 -1.169091364
[46] 2.137454024 0.821786477 0.239238798 -0.002546057 -0.069754554
[51] -0.569073102 -0.537882774 -0.399935908 -0.954161489 -1.048505676
[56] 0.420924922 -0.934108755 -0.973720790 -1.743805839 -0.931596305
[61] -1.939373629 -0.811586391 -0.566087775 1.076834851 0.765556339
[66] 1.567655274 0.162180643 -0.180988275 1.472835439 0.787518121
[71] 0.941836751 0.000571892 0.907848711 0.341258987 1.270600646
[76] -0.648134786 -0.833374007 -0.804929848 -0.048313370 -0.419910646
[81] -0.571045815 -0.108912474 1.535316801 -0.148706057 -1.348683009
[86] -0.321913951 -0.443173589 -0.210393202 -1.434157670 0.186697111
[91] -0.939197297 -0.942039175 -0.706436207 -0.666586761 -0.279622579
[96] -1.521853885 -2.140595760 -1.452463238 -0.170935487 -0.700030211
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] 0.06065059 1.271292 0.6794361 -1.225649 1.338045 -0.9161611 1.568303
[2,] 0.06065059 1.271292 0.6794361 -1.225649 1.338045 -0.9161611 1.568303
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] 0.6434666 -1.800964 -0.1960962 -0.4781423 1.493578 -0.9767239 -0.2534137
[2,] 0.6434666 -1.800964 -0.1960962 -0.4781423 1.493578 -0.9767239 -0.2534137
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] -0.02460925 0.3339344 -0.1572332 0.008671321 -0.3584539 0.9679375 -1.62318
[2,] -0.02460925 0.3339344 -0.1572332 0.008671321 -0.3584539 0.9679375 -1.62318
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] 0.4921839 0.1556971 -0.8616051 -1.008442 1.905168 1.393183 -0.7458127
[2,] 0.4921839 0.1556971 -0.8616051 -1.008442 1.905168 1.393183 -0.7458127
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] 1.00644 0.1149912 2.172002 -0.7519135 0.1807216 -0.9559662 -0.05327793
[2,] 1.00644 0.1149912 2.172002 -0.7519135 0.1807216 -0.9559662 -0.05327793
[,36] [,37] [,38] [,39] [,40] [,41]
[1,] -0.3612058 -1.659353 -0.576492 -0.07758315 -0.5813882 -0.5373791
[2,] -0.3612058 -1.659353 -0.576492 -0.07758315 -0.5813882 -0.5373791
[,42] [,43] [,44] [,45] [,46] [,47] [,48]
[1,] -0.5971688 -0.54844 -0.03914703 -1.169091 2.137454 0.8217865 0.2392388
[2,] -0.5971688 -0.54844 -0.03914703 -1.169091 2.137454 0.8217865 0.2392388
[,49] [,50] [,51] [,52] [,53] [,54]
[1,] -0.002546057 -0.06975455 -0.5690731 -0.5378828 -0.3999359 -0.9541615
[2,] -0.002546057 -0.06975455 -0.5690731 -0.5378828 -0.3999359 -0.9541615
[,55] [,56] [,57] [,58] [,59] [,60] [,61]
[1,] -1.048506 0.4209249 -0.9341088 -0.9737208 -1.743806 -0.9315963 -1.939374
[2,] -1.048506 0.4209249 -0.9341088 -0.9737208 -1.743806 -0.9315963 -1.939374
[,62] [,63] [,64] [,65] [,66] [,67] [,68]
[1,] -0.8115864 -0.5660878 1.076835 0.7655563 1.567655 0.1621806 -0.1809883
[2,] -0.8115864 -0.5660878 1.076835 0.7655563 1.567655 0.1621806 -0.1809883
[,69] [,70] [,71] [,72] [,73] [,74] [,75]
[1,] 1.472835 0.7875181 0.9418368 0.000571892 0.9078487 0.341259 1.270601
[2,] 1.472835 0.7875181 0.9418368 0.000571892 0.9078487 0.341259 1.270601
[,76] [,77] [,78] [,79] [,80] [,81]
[1,] -0.6481348 -0.833374 -0.8049298 -0.04831337 -0.4199106 -0.5710458
[2,] -0.6481348 -0.833374 -0.8049298 -0.04831337 -0.4199106 -0.5710458
[,82] [,83] [,84] [,85] [,86] [,87] [,88]
[1,] -0.1089125 1.535317 -0.1487061 -1.348683 -0.321914 -0.4431736 -0.2103932
[2,] -0.1089125 1.535317 -0.1487061 -1.348683 -0.321914 -0.4431736 -0.2103932
[,89] [,90] [,91] [,92] [,93] [,94] [,95]
[1,] -1.434158 0.1866971 -0.9391973 -0.9420392 -0.7064362 -0.6665868 -0.2796226
[2,] -1.434158 0.1866971 -0.9391973 -0.9420392 -0.7064362 -0.6665868 -0.2796226
[,96] [,97] [,98] [,99] [,100]
[1,] -1.521854 -2.140596 -1.452463 -0.1709355 -0.7000302
[2,] -1.521854 -2.140596 -1.452463 -0.1709355 -0.7000302
>
>
> Max(tmp2)
[1] 2.190699
> Min(tmp2)
[1] -2.535241
> mean(tmp2)
[1] -0.1400584
> Sum(tmp2)
[1] -14.00584
> Var(tmp2)
[1] 1.014879
>
> rowMeans(tmp2)
[1] 0.57946957 -0.20259074 -1.05896017 -0.84464506 0.50736099 -0.08508980
[7] -0.55700041 0.14960251 0.58680835 -0.35222292 0.82948677 -2.35553603
[13] -1.11401969 -0.29636058 -0.50362818 0.25649846 0.07913047 0.60446303
[19] -1.85878823 0.07698617 0.06872066 0.27159467 -1.27345958 -0.58384102
[25] 0.10438255 1.77029874 -0.05049858 0.44338050 -1.52875612 -0.49980910
[31] 0.18846344 1.54132115 -1.16539894 -1.52207996 1.35562369 -0.26942541
[37] 1.71495995 -0.53391223 -1.40843286 0.59826797 -0.39350190 0.27504595
[43] -2.35530178 0.11312895 -0.76403317 0.13797727 0.20279676 -1.03618526
[49] -2.51660066 0.17574627 2.19069936 0.35873359 0.19262556 -0.47554475
[55] 1.71913247 -1.14345320 -0.33665501 0.72241060 0.52519556 0.43162273
[61] -1.31631830 2.08999299 -0.02759839 0.15207703 1.99982320 0.92129169
[67] -1.55375697 -0.10381243 -0.15893250 -2.53524075 0.20960476 -1.47431064
[73] -0.18132462 0.05740962 -0.16164680 0.44491291 0.77749952 -0.16314137
[79] 0.49701076 -1.79363905 -1.01043177 -0.37087617 -0.46704665 -0.79780817
[85] -0.44560898 0.42183462 -0.75210522 -0.74081270 0.70860234 1.20099674
[91] -0.45560369 1.40862115 0.79506051 0.44195540 -1.34498367 0.71524494
[97] 0.54885609 -1.25003222 -1.46233964 -0.51546401
> rowSums(tmp2)
[1] 0.57946957 -0.20259074 -1.05896017 -0.84464506 0.50736099 -0.08508980
[7] -0.55700041 0.14960251 0.58680835 -0.35222292 0.82948677 -2.35553603
[13] -1.11401969 -0.29636058 -0.50362818 0.25649846 0.07913047 0.60446303
[19] -1.85878823 0.07698617 0.06872066 0.27159467 -1.27345958 -0.58384102
[25] 0.10438255 1.77029874 -0.05049858 0.44338050 -1.52875612 -0.49980910
[31] 0.18846344 1.54132115 -1.16539894 -1.52207996 1.35562369 -0.26942541
[37] 1.71495995 -0.53391223 -1.40843286 0.59826797 -0.39350190 0.27504595
[43] -2.35530178 0.11312895 -0.76403317 0.13797727 0.20279676 -1.03618526
[49] -2.51660066 0.17574627 2.19069936 0.35873359 0.19262556 -0.47554475
[55] 1.71913247 -1.14345320 -0.33665501 0.72241060 0.52519556 0.43162273
[61] -1.31631830 2.08999299 -0.02759839 0.15207703 1.99982320 0.92129169
[67] -1.55375697 -0.10381243 -0.15893250 -2.53524075 0.20960476 -1.47431064
[73] -0.18132462 0.05740962 -0.16164680 0.44491291 0.77749952 -0.16314137
[79] 0.49701076 -1.79363905 -1.01043177 -0.37087617 -0.46704665 -0.79780817
[85] -0.44560898 0.42183462 -0.75210522 -0.74081270 0.70860234 1.20099674
[91] -0.45560369 1.40862115 0.79506051 0.44195540 -1.34498367 0.71524494
[97] 0.54885609 -1.25003222 -1.46233964 -0.51546401
> 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] 0.57946957 -0.20259074 -1.05896017 -0.84464506 0.50736099 -0.08508980
[7] -0.55700041 0.14960251 0.58680835 -0.35222292 0.82948677 -2.35553603
[13] -1.11401969 -0.29636058 -0.50362818 0.25649846 0.07913047 0.60446303
[19] -1.85878823 0.07698617 0.06872066 0.27159467 -1.27345958 -0.58384102
[25] 0.10438255 1.77029874 -0.05049858 0.44338050 -1.52875612 -0.49980910
[31] 0.18846344 1.54132115 -1.16539894 -1.52207996 1.35562369 -0.26942541
[37] 1.71495995 -0.53391223 -1.40843286 0.59826797 -0.39350190 0.27504595
[43] -2.35530178 0.11312895 -0.76403317 0.13797727 0.20279676 -1.03618526
[49] -2.51660066 0.17574627 2.19069936 0.35873359 0.19262556 -0.47554475
[55] 1.71913247 -1.14345320 -0.33665501 0.72241060 0.52519556 0.43162273
[61] -1.31631830 2.08999299 -0.02759839 0.15207703 1.99982320 0.92129169
[67] -1.55375697 -0.10381243 -0.15893250 -2.53524075 0.20960476 -1.47431064
[73] -0.18132462 0.05740962 -0.16164680 0.44491291 0.77749952 -0.16314137
[79] 0.49701076 -1.79363905 -1.01043177 -0.37087617 -0.46704665 -0.79780817
[85] -0.44560898 0.42183462 -0.75210522 -0.74081270 0.70860234 1.20099674
[91] -0.45560369 1.40862115 0.79506051 0.44195540 -1.34498367 0.71524494
[97] 0.54885609 -1.25003222 -1.46233964 -0.51546401
> rowMin(tmp2)
[1] 0.57946957 -0.20259074 -1.05896017 -0.84464506 0.50736099 -0.08508980
[7] -0.55700041 0.14960251 0.58680835 -0.35222292 0.82948677 -2.35553603
[13] -1.11401969 -0.29636058 -0.50362818 0.25649846 0.07913047 0.60446303
[19] -1.85878823 0.07698617 0.06872066 0.27159467 -1.27345958 -0.58384102
[25] 0.10438255 1.77029874 -0.05049858 0.44338050 -1.52875612 -0.49980910
[31] 0.18846344 1.54132115 -1.16539894 -1.52207996 1.35562369 -0.26942541
[37] 1.71495995 -0.53391223 -1.40843286 0.59826797 -0.39350190 0.27504595
[43] -2.35530178 0.11312895 -0.76403317 0.13797727 0.20279676 -1.03618526
[49] -2.51660066 0.17574627 2.19069936 0.35873359 0.19262556 -0.47554475
[55] 1.71913247 -1.14345320 -0.33665501 0.72241060 0.52519556 0.43162273
[61] -1.31631830 2.08999299 -0.02759839 0.15207703 1.99982320 0.92129169
[67] -1.55375697 -0.10381243 -0.15893250 -2.53524075 0.20960476 -1.47431064
[73] -0.18132462 0.05740962 -0.16164680 0.44491291 0.77749952 -0.16314137
[79] 0.49701076 -1.79363905 -1.01043177 -0.37087617 -0.46704665 -0.79780817
[85] -0.44560898 0.42183462 -0.75210522 -0.74081270 0.70860234 1.20099674
[91] -0.45560369 1.40862115 0.79506051 0.44195540 -1.34498367 0.71524494
[97] 0.54885609 -1.25003222 -1.46233964 -0.51546401
>
> colMeans(tmp2)
[1] -0.1400584
> colSums(tmp2)
[1] -14.00584
> colVars(tmp2)
[1] 1.014879
> colSd(tmp2)
[1] 1.007412
> colMax(tmp2)
[1] 2.190699
> colMin(tmp2)
[1] -2.535241
> colMedians(tmp2)
[1] -0.06779419
> colRanges(tmp2)
[,1]
[1,] -2.535241
[2,] 2.190699
>
> 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] -3.513505 -1.194881 -5.176298 -4.875840 1.086807 2.153747 -3.872894
[8] -2.746589 -2.938789 -1.044368
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.9505438
[2,] -0.7810189
[3,] -0.4036529
[4,] 0.2671455
[5,] 0.7026233
>
> rowApply(tmp,sum)
[1] 0.2875155 1.4935823 -3.1935436 -1.0835202 -2.7055634 -5.0686652
[7] -4.7415287 -3.2003013 -3.0513799 -0.8592064
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 7 1 7 9 4 5 5 7 5 1
[2,] 2 9 6 2 2 9 6 3 10 6
[3,] 9 2 8 3 10 3 1 4 4 2
[4,] 8 6 9 6 1 1 3 5 6 7
[5,] 10 8 2 1 9 10 9 9 2 5
[6,] 4 3 10 10 6 2 10 10 8 8
[7,] 3 4 3 7 5 8 8 2 3 3
[8,] 6 7 4 8 7 6 7 1 1 4
[9,] 1 10 1 5 8 4 2 6 9 10
[10,] 5 5 5 4 3 7 4 8 7 9
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] 0.50449904 0.02154714 2.19249101 0.73161687 0.52988785 -0.96187420
[7] -0.65825079 2.09175270 0.24310463 0.05193772 0.79315753 2.23399279
[13] 0.84036496 -1.01932512 -1.21047793 -0.61370135 -4.02948880 2.06149992
[19] 1.63316983 2.65345504
> colApply(tmp,quantile)[,1]
[,1]
[1,] -2.18707866
[2,] -0.04277978
[3,] -0.02721028
[4,] 1.12219658
[5,] 1.63937118
>
> rowApply(tmp,sum)
[1] 6.742388 5.292731 -0.842460 2.636683 -5.739984
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 17 2 13 20 13
[2,] 8 18 12 2 10
[3,] 16 1 20 19 15
[4,] 13 14 5 9 12
[5,] 3 9 17 17 4
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 1.12219658 0.07359017 1.1134805 0.75001602 -0.8871456 -0.1290546
[2,] -2.18707866 1.77143839 -2.6553165 0.82367880 0.3167999 0.2383350
[3,] -0.02721028 -0.11689653 2.1730848 -0.73589559 0.7842892 -0.6804857
[4,] 1.63937118 -1.41907208 1.3502170 -0.04457673 1.1427715 0.2708902
[5,] -0.04277978 -0.28751281 0.2110251 -0.06160563 -0.8268271 -0.6615591
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] 0.27896870 0.08691604 1.3862863 -0.9162569 -0.9957193 1.9488234
[2,] 0.64589604 0.91222530 -0.9630558 0.8582583 0.3511896 0.2020436
[3,] -0.32819081 -0.12657632 -0.4144765 0.3065639 0.3752702 0.7241460
[4,] -1.33577255 0.19182637 0.7752985 0.6900713 -0.3780615 -0.5375160
[5,] 0.08084783 1.02736132 -0.5409478 -0.8866988 1.4404786 -0.1035042
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] -0.1032494 0.2583310 1.0391304 -0.08808275 0.1837682 1.2220080
[2,] 0.4125077 1.1795780 -0.3079553 0.36115350 -1.6488991 1.9012710
[3,] -0.4700437 -1.1149038 1.0787162 -0.88635048 -0.5397979 -1.2722639
[4,] 0.7385654 -0.5443065 -1.6045156 0.70023928 0.8934774 -0.4241319
[5,] 0.2625850 -0.7980239 -1.4158536 -0.70066090 -2.9180374 0.6346168
[,19] [,20]
[1,] -0.5391730 0.9375541
[2,] 0.1919867 2.8886749
[3,] 1.2970306 -0.8684695
[4,] 1.1558680 -0.6239597
[5,] -0.4725425 0.3196553
>
>
> 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 : 647 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 : 562 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 1.466655 1.058196 0.7891892 -1.046597 -1.305657 1.016037 -0.4378096
col8 col9 col10 col11 col12 col13 col14
row1 0.4943984 -0.1083125 -1.867465 -0.9733094 -0.2688094 0.9056597 -2.151532
col15 col16 col17 col18 col19 col20
row1 1.283068 -0.2307714 1.201195 2.31634 -0.5360529 -0.5922478
> tmp[,"col10"]
col10
row1 -1.8674646
row2 0.9826119
row3 0.1496636
row4 -0.8288303
row5 2.5481058
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7
row1 1.466655 1.0581959 0.7891892 -1.0465972 -1.305657 1.0160370 -0.4378096
row5 2.138728 -0.1616091 1.0090244 -0.9719937 -2.582789 -0.7541689 0.3706998
col8 col9 col10 col11 col12 col13
row1 0.4943984 -0.1083125 -1.867465 -0.9733094 -0.2688094 0.9056597
row5 1.9804609 -2.4568027 2.548106 -0.3503384 1.3702032 -0.4997650
col14 col15 col16 col17 col18 col19
row1 -2.15153231 1.283067717 -0.2307714 1.201195 2.3163401 -0.5360529
row5 -0.07504611 0.006050957 -0.5114903 -1.335314 -0.6777244 -0.2232351
col20
row1 -0.5922478
row5 0.3255497
> tmp[,c("col6","col20")]
col6 col20
row1 1.0160370 -0.59224778
row2 0.1066467 -0.07322409
row3 -0.5436568 -1.17252433
row4 -0.2355820 1.33279875
row5 -0.7541689 0.32554975
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 1.0160370 -0.5922478
row5 -0.7541689 0.3255497
>
>
>
>
> tmp["row1",] <- rnorm(20,mean=10)
> tmp[,"col10"] <- rnorm(5,mean=30)
> tmp[c("row1","row5"),] <- rnorm(40,mean=50)
> tmp[,c("col6","col20")] <- rnorm(10,mean=75)
> tmp[c("row1","row5"),c("col6","col20")] <- rnorm(4,mean=105)
>
> tmp["row1",]
col1 col2 col3 col4 col5 col6 col7 col8
row1 50.59226 48.86603 49.95349 51.22642 49.74786 106.273 50.6387 49.87816
col9 col10 col11 col12 col13 col14 col15 col16
row1 50.68181 47.34531 50.4346 48.75779 50.04559 49.97548 50.6908 50.79615
col17 col18 col19 col20
row1 51.63785 49.70516 49.53023 103.7586
> tmp[,"col10"]
col10
row1 47.34531
row2 29.56657
row3 28.62252
row4 28.02495
row5 48.77087
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 50.59226 48.86603 49.95349 51.22642 49.74786 106.2730 50.63870 49.87816
row5 50.48151 49.29570 50.34649 51.96696 50.28188 104.0513 49.15128 48.61641
col9 col10 col11 col12 col13 col14 col15 col16
row1 50.68181 47.34531 50.43460 48.75779 50.04559 49.97548 50.69080 50.79615
row5 47.06994 48.77087 51.03656 49.56029 49.13768 49.82315 49.16841 51.04107
col17 col18 col19 col20
row1 51.63785 49.70516 49.53023 103.7586
row5 50.92924 47.98652 49.96584 104.6536
> tmp[,c("col6","col20")]
col6 col20
row1 106.27297 103.75860
row2 75.32637 75.00873
row3 74.16859 75.19736
row4 75.31606 74.58170
row5 104.05131 104.65364
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 106.2730 103.7586
row5 104.0513 104.6536
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 106.2730 103.7586
row5 104.0513 104.6536
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] 0.6079828
[2,] -0.4682212
[3,] 0.2004389
[4,] -0.5438641
[5,] 1.0303381
> tmp[,c("col17","col7")]
col17 col7
[1,] -0.11160963 0.453489243
[2,] -1.16999262 -1.882149762
[3,] -0.44265770 -0.732149027
[4,] -0.02238686 0.003666635
[5,] -0.86272821 0.436462965
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] 0.8374633 -1.60997161
[2,] 0.4357901 -0.79028327
[3,] 0.1965482 1.07325368
[4,] 0.7555705 0.30824317
[5,] 1.0514375 -0.06359407
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] 0.8374633
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] 0.8374633
[2,] 0.4357901
>
>
>
> 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 0.1909827 -0.2653792 2.81421499 1.0097180 0.51136791 -1.627291 0.6575945
row1 0.3329370 1.6475500 0.06500692 0.4435872 -0.02508171 -1.552179 1.2199965
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row3 0.01743517 0.9381232 1.552542 -1.3138193 -0.7908346 0.6182120 -1.2970723
row1 1.05234173 0.4918493 -2.266995 0.2868645 0.9007936 0.3131449 0.1173005
[,15] [,16] [,17] [,18] [,19] [,20]
row3 0.9260780 -0.2754361 -0.4617465 -0.0825108 0.2807765 -0.2852588
row1 -0.6072834 -0.3761158 0.1566137 -0.8995844 -0.1737898 1.2788078
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 -1.12444 0.152198 -1.045417 0.2252173 -1.223223 1.102816 0.9421336
[,8] [,9] [,10]
row2 -0.01547206 -0.3772614 -1.034301
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 -1.465499 1.161777 0.08195542 -1.093472 1.298106 0.1358506 0.04360441
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 -0.5019657 -2.260265 0.9245897 0.4804224 -0.02542874 0.63713 -0.01481584
[,15] [,16] [,17] [,18] [,19] [,20]
row5 -0.1496718 -1.244054 -0.830024 0.2104951 -0.008567419 -0.2943188
>
>
> 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: 0x628a4f8bfba0>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMcd2282cc49f4b"
[2] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMcd2281b592d67"
[3] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMcd2284fab06c"
[4] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMcd228568404b2"
[5] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMcd22854c0e251"
[6] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMcd228730d1a5b"
[7] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMcd2283e1b28ca"
[8] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMcd22875e4379c"
[9] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMcd22831988a14"
[10] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMcd228168cede7"
[11] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMcd2283dba7d9f"
[12] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMcd22819e32cd1"
[13] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMcd228c781290"
[14] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMcd22868244c00"
[15] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BMcd22853b4431d"
>
>
> ### 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: 0x628a516016f0>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x628a516016f0>
Warning message:
In dir.create(new.directory) :
'/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x628a516016f0>
> rowMedians(tmp)
[1] -0.338411009 -0.098101604 0.069875604 0.330404908 -0.235720212
[6] 0.009252994 0.052457006 0.024250123 0.382110506 0.514741099
[11] 0.233054021 0.201429672 0.116806676 -0.061358714 0.404526745
[16] 0.158118728 -0.038714295 0.089190523 -0.352241511 0.410951147
[21] 0.177834863 -0.513439324 0.493394108 0.232449120 -0.303242373
[26] 0.635992303 0.506524689 0.282040290 0.231370890 0.002836806
[31] -0.637407621 0.425748033 0.276183615 0.056724464 0.549742392
[36] 0.008368447 -0.427381929 -0.635740551 0.488643598 0.068869339
[41] 0.069006777 0.175930752 0.093391449 0.464139973 0.495779507
[46] -0.275838075 -0.118035903 -0.160827307 0.151713742 -0.065689743
[51] -0.459890609 -0.340080426 0.312318991 0.050258326 -0.222761923
[56] 0.263945099 0.143796337 0.294017427 0.248722969 0.123845568
[61] 0.032163853 0.084815740 -0.126200039 -0.230889151 0.362354393
[66] -0.266350463 0.141634527 -0.280839871 0.044995246 0.220868816
[71] 0.173985725 0.176722751 -0.218794559 0.001903444 0.820684785
[76] 0.526495516 0.050823656 0.316316888 0.512646170 -0.155780051
[81] 0.278264625 0.529590846 -0.455355905 -0.029472185 -0.361280257
[86] -0.490104413 0.007738300 0.241151422 0.152122254 0.498802645
[91] 0.090041221 0.165139091 0.212093160 0.339629435 -0.090520692
[96] 0.347042412 -0.258523370 0.045403123 0.267622032 0.037056108
[101] -0.090850617 0.098926359 -0.089926964 0.047945389 -0.114873941
[106] -0.219752764 0.049673269 0.606853541 0.228887531 0.062263415
[111] -0.002158011 0.015741654 -0.315281860 0.171006125 0.230650047
[116] -0.338570664 0.303076190 -0.037742888 -0.392420441 0.261963415
[121] 0.331303253 0.675927097 -0.119078027 0.057314743 -0.194741706
[126] -0.136400287 -0.125747122 -0.445205345 -0.268611232 0.649779131
[131] -0.527975617 -0.442936733 -0.029281791 -0.074664523 0.042007934
[136] 0.558152304 -0.363134718 -0.007748098 -0.010991920 0.783852399
[141] -0.231246091 0.035273219 0.172811649 -0.017872778 -0.367203477
[146] -0.077842065 -0.298830832 -0.189097077 -0.297614344 -0.419997833
[151] 0.704742057 -0.412872785 -0.003764499 -0.461273364 0.098439654
[156] 0.238302647 0.533228411 0.065712281 0.340956516 -0.146377279
[161] -0.026747835 0.174146044 -0.227174214 0.224919336 0.093858685
[166] 0.069326037 -0.125747063 0.575690528 0.099286587 0.070487713
[171] 0.443890013 0.118315723 -0.449023913 0.107395016 -0.056716939
[176] -0.234399357 -0.433128972 -0.178834581 -0.333390663 -0.244796747
[181] -0.041192913 0.730607948 0.356647033 0.244373116 -0.874849493
[186] 0.275905919 -0.127827209 0.116649571 -0.294381445 0.221960416
[191] -0.354267058 0.325628960 -0.039124335 0.309920140 0.109777617
[196] 0.363634871 -0.128300112 0.155395481 0.144474331 0.149746375
[201] -0.077738274 -0.119386077 -0.763491204 -0.575795929 -0.423856127
[206] -0.009299405 -0.006539365 0.506862174 -0.240758471 0.018673983
[211] -0.626457075 0.553979080 0.269593375 -0.578614328 0.209249588
[216] 0.049852033 0.493260468 0.001791141 0.089902584 -0.284259418
[221] -0.386787887 -0.206118797 0.040412883 -0.102012322 -0.079954542
[226] -0.162801101 -0.614187843 0.098520640 0.478202202 -0.075175756
>
> proc.time()
user system elapsed
1.268 0.658 1.912
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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: 0x613c759831c0>
> .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: 0x613c759831c0>
> .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: 0x613c759831c0>
> .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: 0x613c759831c0>
> 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: 0x613c75c66120>
> .Call("R_bm_AddColumn",P)
<pointer: 0x613c75c66120>
> .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: 0x613c75c66120>
> .Call("R_bm_AddColumn",P)
<pointer: 0x613c75c66120>
> .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: 0x613c75c66120>
> 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: 0x613c7491a4a0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x613c7491a4a0>
> .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: 0x613c7491a4a0>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x613c7491a4a0>
> .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: 0x613c7491a4a0>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x613c7491a4a0>
> .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: 0x613c7491a4a0>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x613c7491a4a0>
> .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: 0x613c7491a4a0>
> 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: 0x613c749b6390>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x613c749b6390>
> .Call("R_bm_AddColumn",P)
<pointer: 0x613c749b6390>
> .Call("R_bm_AddColumn",P)
<pointer: 0x613c749b6390>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFilecd2cc110ed402" "BufferedMatrixFilecd2cc67a84ab5"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFilecd2cc110ed402" "BufferedMatrixFilecd2cc67a84ab5"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x613c75235650>
> .Call("R_bm_AddColumn",P)
<pointer: 0x613c75235650>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x613c75235650>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x613c75235650>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x613c75235650>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x613c75235650>
> .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: 0x613c763bc430>
> .Call("R_bm_AddColumn",P)
<pointer: 0x613c763bc430>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x613c763bc430>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x613c763bc430>
> 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: 0x613c766b1250>
> .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: 0x613c766b1250>
> rm(P)
>
> proc.time()
user system elapsed
0.246 0.043 0.277
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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Platform: x86_64-pc-linux-gnu
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You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
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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
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> library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths());
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
>
> Temp <- createBufferedMatrix(100)
> dim(Temp)
[1] 100 0
> buffer.dim(Temp)
[1] 1 1
>
>
> proc.time()
user system elapsed
0.261 0.045 0.294