Ben Bolstad
| Snapshot Date: 2026-03-29 13:45 -0400 (Sun, 29 Mar 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 -0400 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-03-30 11:57 -0400 (Mon, 30 Mar 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" | 4893 |
| 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: 2026-03-29 22:07:36 -0400 (Sun, 29 Mar 2026) |
| EndedAt: 2026-03-29 22:08:00 -0400 (Sun, 29 Mar 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 24.04.4 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 13.3.0-6ubuntu2~24.04.1) 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 13.3.0-6ubuntu2~24.04.1) 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
0.272 0.050 0.308
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] "Sun Mar 29 22:07:51 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] "Sun Mar 29 22:07:51 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: 0x58f9a940a1c0>
>
>
>
> 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] "Sun Mar 29 22:07:51 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] "Sun Mar 29 22:07:51 2026"
>
> ColMode(tmp2)
<pointer: 0x58f9a940a1c0>
>
>
>
> ### 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,] 98.7780605 0.3365572 0.399539 -1.2133109
[2,] 1.0626493 1.2056022 -0.744217 0.5866972
[3,] 1.1747944 -0.1985672 -1.460474 0.9505825
[4,] -0.3035402 1.2947160 -1.582634 -1.2684199
> 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,] 98.7780605 0.3365572 0.399539 1.2133109
[2,] 1.0626493 1.2056022 0.744217 0.5866972
[3,] 1.1747944 0.1985672 1.460474 0.9505825
[4,] 0.3035402 1.2947160 1.582634 1.2684199
> 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,] 9.9387152 0.5801355 0.6320910 1.1015039
[2,] 1.0308488 1.0979992 0.8626801 0.7659616
[3,] 1.0838793 0.4456088 1.2085009 0.9749782
[4,] 0.5509448 1.1378559 1.2580278 1.1262415
>
> 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,] 223.16521 31.13791 31.72045 37.22835
[2,] 36.37114 37.18559 34.37102 33.24631
[3,] 37.01359 29.65466 38.54548 35.70036
[4,] 30.81299 37.67327 39.16291 37.53083
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x58f9aa0108b0>
> exp(tmp5)
<pointer: 0x58f9aa0108b0>
> log(tmp5,2)
<pointer: 0x58f9aa0108b0>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 464.4892
> Min(tmp5)
[1] 55.56308
> mean(tmp5)
[1] 72.44907
> Sum(tmp5)
[1] 14489.81
> Var(tmp5)
[1] 837.8338
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 91.42477 70.82163 71.30286 71.50894 70.42686 73.10651 70.90167 69.83498
[9] 67.14936 68.01309
> rowSums(tmp5)
[1] 1828.495 1416.433 1426.057 1430.179 1408.537 1462.130 1418.033 1396.700
[9] 1342.987 1360.262
> rowVars(tmp5)
[1] 7768.47634 61.30915 76.95513 40.64033 53.54241 73.41257
[7] 65.00936 98.92422 60.31761 27.73725
> rowSd(tmp5)
[1] 88.138960 7.830016 8.772407 6.374977 7.317268 8.568114 8.062838
[8] 9.946066 7.766441 5.266616
> rowMax(tmp5)
[1] 464.48915 84.54308 95.78206 81.51247 85.27524 91.27931 87.00976
[8] 93.49358 82.47221 79.06341
> rowMin(tmp5)
[1] 59.60134 55.98530 55.56308 60.87776 55.64236 60.06323 56.96838 55.59160
[9] 55.67215 57.49165
>
> colMeans(tmp5)
[1] 107.36519 69.52686 70.56330 72.56960 65.50049 65.71612 72.38480
[8] 69.85473 72.91170 66.78835 71.93210 80.52544 70.11991 74.58718
[15] 70.21825 69.89740 69.28947 67.70699 70.92785 70.59562
> colSums(tmp5)
[1] 1073.6519 695.2686 705.6330 725.6960 655.0049 657.1612 723.8480
[8] 698.5473 729.1170 667.8835 719.3210 805.2544 701.1991 745.8718
[15] 702.1825 698.9740 692.8947 677.0699 709.2785 705.9562
> colVars(tmp5)
[1] 15788.79112 74.88894 47.99193 23.73199 44.99538 36.86312
[7] 32.55162 97.28968 49.76852 76.10581 21.35596 81.26617
[13] 63.75113 84.42192 41.54318 82.17030 69.89174 43.06891
[19] 34.22286 76.26305
> colSd(tmp5)
[1] 125.653456 8.653840 6.927621 4.871549 6.707860 6.071501
[7] 5.705402 9.863553 7.054680 8.723864 4.621251 9.014775
[13] 7.984431 9.188140 6.445400 9.064784 8.360128 6.562691
[19] 5.850031 8.732872
> colMax(tmp5)
[1] 464.48915 79.55660 81.51247 80.96125 80.20958 75.50148 80.18739
[8] 84.95584 87.00976 85.27524 80.60225 95.78206 83.67461 91.27931
[15] 79.26425 82.33521 84.54308 77.57346 80.41752 84.43930
> colMin(tmp5)
[1] 59.59360 56.96838 60.30268 67.11620 55.64236 57.00407 63.44579 55.59160
[9] 63.76693 56.50008 64.37974 66.91750 59.96716 62.94344 55.98530 55.56308
[17] 55.90439 55.67215 62.35037 55.68494
>
>
> ### 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] 91.42477 70.82163 71.30286 71.50894 70.42686 NA 70.90167 69.83498
[9] 67.14936 68.01309
> rowSums(tmp5)
[1] 1828.495 1416.433 1426.057 1430.179 1408.537 NA 1418.033 1396.700
[9] 1342.987 1360.262
> rowVars(tmp5)
[1] 7768.47634 61.30915 76.95513 40.64033 53.54241 76.34032
[7] 65.00936 98.92422 60.31761 27.73725
> rowSd(tmp5)
[1] 88.138960 7.830016 8.772407 6.374977 7.317268 8.737295 8.062838
[8] 9.946066 7.766441 5.266616
> rowMax(tmp5)
[1] 464.48915 84.54308 95.78206 81.51247 85.27524 NA 87.00976
[8] 93.49358 82.47221 79.06341
> rowMin(tmp5)
[1] 59.60134 55.98530 55.56308 60.87776 55.64236 NA 56.96838 55.59160
[9] 55.67215 57.49165
>
> colMeans(tmp5)
[1] 107.36519 69.52686 70.56330 72.56960 65.50049 65.71612 72.38480
[8] 69.85473 72.91170 66.78835 71.93210 80.52544 70.11991 74.58718
[15] 70.21825 69.89740 NA 67.70699 70.92785 70.59562
> colSums(tmp5)
[1] 1073.6519 695.2686 705.6330 725.6960 655.0049 657.1612 723.8480
[8] 698.5473 729.1170 667.8835 719.3210 805.2544 701.1991 745.8718
[15] 702.1825 698.9740 NA 677.0699 709.2785 705.9562
> colVars(tmp5)
[1] 15788.79112 74.88894 47.99193 23.73199 44.99538 36.86312
[7] 32.55162 97.28968 49.76852 76.10581 21.35596 81.26617
[13] 63.75113 84.42192 41.54318 82.17030 NA 43.06891
[19] 34.22286 76.26305
> colSd(tmp5)
[1] 125.653456 8.653840 6.927621 4.871549 6.707860 6.071501
[7] 5.705402 9.863553 7.054680 8.723864 4.621251 9.014775
[13] 7.984431 9.188140 6.445400 9.064784 NA 6.562691
[19] 5.850031 8.732872
> colMax(tmp5)
[1] 464.48915 79.55660 81.51247 80.96125 80.20958 75.50148 80.18739
[8] 84.95584 87.00976 85.27524 80.60225 95.78206 83.67461 91.27931
[15] 79.26425 82.33521 NA 77.57346 80.41752 84.43930
> colMin(tmp5)
[1] 59.59360 56.96838 60.30268 67.11620 55.64236 57.00407 63.44579 55.59160
[9] 63.76693 56.50008 64.37974 66.91750 59.96716 62.94344 55.98530 55.56308
[17] NA 55.67215 62.35037 55.68494
>
> Max(tmp5,na.rm=TRUE)
[1] 464.4892
> Min(tmp5,na.rm=TRUE)
[1] 55.56308
> mean(tmp5,na.rm=TRUE)
[1] 72.42347
> Sum(tmp5,na.rm=TRUE)
[1] 14412.27
> Var(tmp5,na.rm=TRUE)
[1] 841.9336
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 91.42477 70.82163 71.30286 71.50894 70.42686 72.87304 70.90167 69.83498
[9] 67.14936 68.01309
> rowSums(tmp5,na.rm=TRUE)
[1] 1828.495 1416.433 1426.057 1430.179 1408.537 1384.588 1418.033 1396.700
[9] 1342.987 1360.262
> rowVars(tmp5,na.rm=TRUE)
[1] 7768.47634 61.30915 76.95513 40.64033 53.54241 76.34032
[7] 65.00936 98.92422 60.31761 27.73725
> rowSd(tmp5,na.rm=TRUE)
[1] 88.138960 7.830016 8.772407 6.374977 7.317268 8.737295 8.062838
[8] 9.946066 7.766441 5.266616
> rowMax(tmp5,na.rm=TRUE)
[1] 464.48915 84.54308 95.78206 81.51247 85.27524 91.27931 87.00976
[8] 93.49358 82.47221 79.06341
> rowMin(tmp5,na.rm=TRUE)
[1] 59.60134 55.98530 55.56308 60.87776 55.64236 60.06323 56.96838 55.59160
[9] 55.67215 57.49165
>
> colMeans(tmp5,na.rm=TRUE)
[1] 107.36519 69.52686 70.56330 72.56960 65.50049 65.71612 72.38480
[8] 69.85473 72.91170 66.78835 71.93210 80.52544 70.11991 74.58718
[15] 70.21825 69.89740 68.37248 67.70699 70.92785 70.59562
> colSums(tmp5,na.rm=TRUE)
[1] 1073.6519 695.2686 705.6330 725.6960 655.0049 657.1612 723.8480
[8] 698.5473 729.1170 667.8835 719.3210 805.2544 701.1991 745.8718
[15] 702.1825 698.9740 615.3523 677.0699 709.2785 705.9562
> colVars(tmp5,na.rm=TRUE)
[1] 15788.79112 74.88894 47.99193 23.73199 44.99538 36.86312
[7] 32.55162 97.28968 49.76852 76.10581 21.35596 81.26617
[13] 63.75113 84.42192 41.54318 82.17030 69.16832 43.06891
[19] 34.22286 76.26305
> colSd(tmp5,na.rm=TRUE)
[1] 125.653456 8.653840 6.927621 4.871549 6.707860 6.071501
[7] 5.705402 9.863553 7.054680 8.723864 4.621251 9.014775
[13] 7.984431 9.188140 6.445400 9.064784 8.316749 6.562691
[19] 5.850031 8.732872
> colMax(tmp5,na.rm=TRUE)
[1] 464.48915 79.55660 81.51247 80.96125 80.20958 75.50148 80.18739
[8] 84.95584 87.00976 85.27524 80.60225 95.78206 83.67461 91.27931
[15] 79.26425 82.33521 84.54308 77.57346 80.41752 84.43930
> colMin(tmp5,na.rm=TRUE)
[1] 59.59360 56.96838 60.30268 67.11620 55.64236 57.00407 63.44579 55.59160
[9] 63.76693 56.50008 64.37974 66.91750 59.96716 62.94344 55.98530 55.56308
[17] 55.90439 55.67215 62.35037 55.68494
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 91.42477 70.82163 71.30286 71.50894 70.42686 NaN 70.90167 69.83498
[9] 67.14936 68.01309
> rowSums(tmp5,na.rm=TRUE)
[1] 1828.495 1416.433 1426.057 1430.179 1408.537 0.000 1418.033 1396.700
[9] 1342.987 1360.262
> rowVars(tmp5,na.rm=TRUE)
[1] 7768.47634 61.30915 76.95513 40.64033 53.54241 NA
[7] 65.00936 98.92422 60.31761 27.73725
> rowSd(tmp5,na.rm=TRUE)
[1] 88.138960 7.830016 8.772407 6.374977 7.317268 NA 8.062838
[8] 9.946066 7.766441 5.266616
> rowMax(tmp5,na.rm=TRUE)
[1] 464.48915 84.54308 95.78206 81.51247 85.27524 NA 87.00976
[8] 93.49358 82.47221 79.06341
> rowMin(tmp5,na.rm=TRUE)
[1] 59.60134 55.98530 55.56308 60.87776 55.64236 NA 56.96838 55.59160
[9] 55.67215 57.49165
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 112.31135 69.72548 71.70337 71.63719 65.54711 66.34422 72.22235
[8] 68.17683 73.92779 65.87987 72.01422 81.04591 68.61383 72.73250
[15] 69.87904 69.06370 NaN 67.96699 70.28456 70.07158
> colSums(tmp5,na.rm=TRUE)
[1] 1010.8021 627.5293 645.3303 644.7347 589.9240 597.0980 650.0011
[8] 613.5915 665.3501 592.9188 648.1280 729.4132 617.5245 654.5925
[15] 628.9114 621.5733 0.0000 611.7029 632.5611 630.6442
> colVars(tmp5,na.rm=TRUE)
[1] 17487.16435 83.80628 39.36866 16.91795 50.59535 37.03279
[7] 36.32367 77.77819 44.37473 76.33388 23.94958 88.37696
[13] 46.20198 56.27643 45.44165 84.62220 NA 47.69202
[19] 33.84533 82.70647
> colSd(tmp5,na.rm=TRUE)
[1] 132.239042 9.154577 6.274445 4.113144 7.113041 6.085457
[7] 6.026912 8.819194 6.661436 8.736926 4.893831 9.400902
[13] 6.797204 7.501762 6.741042 9.199032 NA 6.905941
[19] 5.817674 9.094310
> colMax(tmp5,na.rm=TRUE)
[1] 464.48915 79.55660 81.51247 78.11552 80.20958 75.50148 80.18739
[8] 81.23210 87.00976 85.27524 80.60225 95.78206 80.31854 83.31797
[15] 79.26425 82.33521 -Inf 77.57346 80.41752 84.43930
> colMin(tmp5,na.rm=TRUE)
[1] 59.59360 56.96838 62.59873 67.11620 55.64236 57.00407 63.44579 55.59160
[9] 66.14407 56.50008 64.37974 66.91750 59.96716 62.94344 55.98530 55.56308
[17] Inf 55.67215 62.35037 55.68494
>
>
>
>
> 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] 264.1460 173.4101 222.0698 269.4641 105.3193 292.4116 316.1171 104.7248
[9] 219.8805 193.3443
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 264.1460 173.4101 222.0698 269.4641 105.3193 292.4116 316.1171 104.7248
[9] 219.8805 193.3443
>
>
>
> copymatrix <- matrix(rnorm(200,150,15),10,20)
>
> tmp5[1:10,1:20] <- copymatrix
> which.row <- 1
> which.col <- 3
> cat(which.row," ",which.col,"\n")
1 3
> tmp5[which.row,which.col] <- NA
> copymatrix[which.row,which.col] <- NA
>
> colVars(tmp5,na.rm=TRUE)-apply(copymatrix,2,var,na.rm=TRUE)
[1] 1.136868e-13 -5.684342e-14 0.000000e+00 -1.705303e-13 1.705303e-13
[6] -3.410605e-13 -5.684342e-14 -2.842171e-14 -1.136868e-13 -1.421085e-14
[11] 1.136868e-13 1.705303e-13 1.705303e-13 2.273737e-13 -1.421085e-13
[16] -2.842171e-14 -1.705303e-13 1.705303e-13 0.000000e+00 -2.842171e-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)
+ }
1 6
9 20
2 9
8 12
4 16
5 4
5 9
6 4
6 7
1 20
9 9
6 19
10 2
6 2
4 13
8 20
10 7
3 6
10 2
5 12
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] 1.937265
> Min(tmp)
[1] -2.755298
> mean(tmp)
[1] -0.006722613
> Sum(tmp)
[1] -0.6722613
> Var(tmp)
[1] 0.8511792
>
> rowMeans(tmp)
[1] -0.006722613
> rowSums(tmp)
[1] -0.6722613
> rowVars(tmp)
[1] 0.8511792
> rowSd(tmp)
[1] 0.9225937
> rowMax(tmp)
[1] 1.937265
> rowMin(tmp)
[1] -2.755298
>
> colMeans(tmp)
[1] 0.237577741 -0.185110119 -0.733245721 0.032702857 0.860493021
[6] 0.056073221 1.937265230 0.039660183 -0.682644795 0.483321920
[11] 0.124193645 0.315485643 -1.064057706 -0.682108605 -0.033414834
[16] 0.610688217 1.437116039 -0.043279458 -0.604459215 -1.301345170
[21] -0.396529561 -0.036814612 -0.465716845 -0.049594307 0.493242135
[26] -0.430556715 0.718572015 -0.393180814 1.627341702 1.098807043
[31] -0.694200902 -1.362403642 -0.304469721 0.716799658 0.315366447
[36] 0.149740200 1.416817346 1.237428081 1.020068990 -0.812305036
[41] -1.446326815 0.782421618 0.532774584 0.209388997 1.014508455
[46] -0.446724627 -2.755298159 -1.260761374 0.800547811 1.297024489
[51] -1.107504449 0.616972516 -0.108784781 0.085291645 0.221002640
[56] 1.202381459 -0.219790114 0.201705591 -0.478231562 0.233886726
[61] -0.892026498 1.602038579 -1.433380248 0.782050848 -1.050928839
[66] 1.644877376 -0.052548964 0.377976538 1.160538825 -0.829674102
[71] -0.887325012 0.140811930 0.791318255 1.452982306 0.319544637
[76] -0.006583557 -1.975595765 -0.424783795 -0.553948391 -0.640602730
[81] -0.358277676 -0.907039705 0.745524360 -0.784337110 1.171892511
[86] -0.752196588 -1.360525365 -0.967740544 -0.834785438 0.593613452
[91] 1.782971452 0.988143720 0.611781614 -1.007157928 -0.258278781
[96] 0.821590701 -1.073862319 -1.775418479 -0.364612007 -0.496096726
> colSums(tmp)
[1] 0.237577741 -0.185110119 -0.733245721 0.032702857 0.860493021
[6] 0.056073221 1.937265230 0.039660183 -0.682644795 0.483321920
[11] 0.124193645 0.315485643 -1.064057706 -0.682108605 -0.033414834
[16] 0.610688217 1.437116039 -0.043279458 -0.604459215 -1.301345170
[21] -0.396529561 -0.036814612 -0.465716845 -0.049594307 0.493242135
[26] -0.430556715 0.718572015 -0.393180814 1.627341702 1.098807043
[31] -0.694200902 -1.362403642 -0.304469721 0.716799658 0.315366447
[36] 0.149740200 1.416817346 1.237428081 1.020068990 -0.812305036
[41] -1.446326815 0.782421618 0.532774584 0.209388997 1.014508455
[46] -0.446724627 -2.755298159 -1.260761374 0.800547811 1.297024489
[51] -1.107504449 0.616972516 -0.108784781 0.085291645 0.221002640
[56] 1.202381459 -0.219790114 0.201705591 -0.478231562 0.233886726
[61] -0.892026498 1.602038579 -1.433380248 0.782050848 -1.050928839
[66] 1.644877376 -0.052548964 0.377976538 1.160538825 -0.829674102
[71] -0.887325012 0.140811930 0.791318255 1.452982306 0.319544637
[76] -0.006583557 -1.975595765 -0.424783795 -0.553948391 -0.640602730
[81] -0.358277676 -0.907039705 0.745524360 -0.784337110 1.171892511
[86] -0.752196588 -1.360525365 -0.967740544 -0.834785438 0.593613452
[91] 1.782971452 0.988143720 0.611781614 -1.007157928 -0.258278781
[96] 0.821590701 -1.073862319 -1.775418479 -0.364612007 -0.496096726
> 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] 0.237577741 -0.185110119 -0.733245721 0.032702857 0.860493021
[6] 0.056073221 1.937265230 0.039660183 -0.682644795 0.483321920
[11] 0.124193645 0.315485643 -1.064057706 -0.682108605 -0.033414834
[16] 0.610688217 1.437116039 -0.043279458 -0.604459215 -1.301345170
[21] -0.396529561 -0.036814612 -0.465716845 -0.049594307 0.493242135
[26] -0.430556715 0.718572015 -0.393180814 1.627341702 1.098807043
[31] -0.694200902 -1.362403642 -0.304469721 0.716799658 0.315366447
[36] 0.149740200 1.416817346 1.237428081 1.020068990 -0.812305036
[41] -1.446326815 0.782421618 0.532774584 0.209388997 1.014508455
[46] -0.446724627 -2.755298159 -1.260761374 0.800547811 1.297024489
[51] -1.107504449 0.616972516 -0.108784781 0.085291645 0.221002640
[56] 1.202381459 -0.219790114 0.201705591 -0.478231562 0.233886726
[61] -0.892026498 1.602038579 -1.433380248 0.782050848 -1.050928839
[66] 1.644877376 -0.052548964 0.377976538 1.160538825 -0.829674102
[71] -0.887325012 0.140811930 0.791318255 1.452982306 0.319544637
[76] -0.006583557 -1.975595765 -0.424783795 -0.553948391 -0.640602730
[81] -0.358277676 -0.907039705 0.745524360 -0.784337110 1.171892511
[86] -0.752196588 -1.360525365 -0.967740544 -0.834785438 0.593613452
[91] 1.782971452 0.988143720 0.611781614 -1.007157928 -0.258278781
[96] 0.821590701 -1.073862319 -1.775418479 -0.364612007 -0.496096726
> colMin(tmp)
[1] 0.237577741 -0.185110119 -0.733245721 0.032702857 0.860493021
[6] 0.056073221 1.937265230 0.039660183 -0.682644795 0.483321920
[11] 0.124193645 0.315485643 -1.064057706 -0.682108605 -0.033414834
[16] 0.610688217 1.437116039 -0.043279458 -0.604459215 -1.301345170
[21] -0.396529561 -0.036814612 -0.465716845 -0.049594307 0.493242135
[26] -0.430556715 0.718572015 -0.393180814 1.627341702 1.098807043
[31] -0.694200902 -1.362403642 -0.304469721 0.716799658 0.315366447
[36] 0.149740200 1.416817346 1.237428081 1.020068990 -0.812305036
[41] -1.446326815 0.782421618 0.532774584 0.209388997 1.014508455
[46] -0.446724627 -2.755298159 -1.260761374 0.800547811 1.297024489
[51] -1.107504449 0.616972516 -0.108784781 0.085291645 0.221002640
[56] 1.202381459 -0.219790114 0.201705591 -0.478231562 0.233886726
[61] -0.892026498 1.602038579 -1.433380248 0.782050848 -1.050928839
[66] 1.644877376 -0.052548964 0.377976538 1.160538825 -0.829674102
[71] -0.887325012 0.140811930 0.791318255 1.452982306 0.319544637
[76] -0.006583557 -1.975595765 -0.424783795 -0.553948391 -0.640602730
[81] -0.358277676 -0.907039705 0.745524360 -0.784337110 1.171892511
[86] -0.752196588 -1.360525365 -0.967740544 -0.834785438 0.593613452
[91] 1.782971452 0.988143720 0.611781614 -1.007157928 -0.258278781
[96] 0.821590701 -1.073862319 -1.775418479 -0.364612007 -0.496096726
> colMedians(tmp)
[1] 0.237577741 -0.185110119 -0.733245721 0.032702857 0.860493021
[6] 0.056073221 1.937265230 0.039660183 -0.682644795 0.483321920
[11] 0.124193645 0.315485643 -1.064057706 -0.682108605 -0.033414834
[16] 0.610688217 1.437116039 -0.043279458 -0.604459215 -1.301345170
[21] -0.396529561 -0.036814612 -0.465716845 -0.049594307 0.493242135
[26] -0.430556715 0.718572015 -0.393180814 1.627341702 1.098807043
[31] -0.694200902 -1.362403642 -0.304469721 0.716799658 0.315366447
[36] 0.149740200 1.416817346 1.237428081 1.020068990 -0.812305036
[41] -1.446326815 0.782421618 0.532774584 0.209388997 1.014508455
[46] -0.446724627 -2.755298159 -1.260761374 0.800547811 1.297024489
[51] -1.107504449 0.616972516 -0.108784781 0.085291645 0.221002640
[56] 1.202381459 -0.219790114 0.201705591 -0.478231562 0.233886726
[61] -0.892026498 1.602038579 -1.433380248 0.782050848 -1.050928839
[66] 1.644877376 -0.052548964 0.377976538 1.160538825 -0.829674102
[71] -0.887325012 0.140811930 0.791318255 1.452982306 0.319544637
[76] -0.006583557 -1.975595765 -0.424783795 -0.553948391 -0.640602730
[81] -0.358277676 -0.907039705 0.745524360 -0.784337110 1.171892511
[86] -0.752196588 -1.360525365 -0.967740544 -0.834785438 0.593613452
[91] 1.782971452 0.988143720 0.611781614 -1.007157928 -0.258278781
[96] 0.821590701 -1.073862319 -1.775418479 -0.364612007 -0.496096726
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] 0.2375777 -0.1851101 -0.7332457 0.03270286 0.860493 0.05607322 1.937265
[2,] 0.2375777 -0.1851101 -0.7332457 0.03270286 0.860493 0.05607322 1.937265
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] 0.03966018 -0.6826448 0.4833219 0.1241936 0.3154856 -1.064058 -0.6821086
[2,] 0.03966018 -0.6826448 0.4833219 0.1241936 0.3154856 -1.064058 -0.6821086
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] -0.03341483 0.6106882 1.437116 -0.04327946 -0.6044592 -1.301345 -0.3965296
[2,] -0.03341483 0.6106882 1.437116 -0.04327946 -0.6044592 -1.301345 -0.3965296
[,22] [,23] [,24] [,25] [,26] [,27]
[1,] -0.03681461 -0.4657168 -0.04959431 0.4932421 -0.4305567 0.718572
[2,] -0.03681461 -0.4657168 -0.04959431 0.4932421 -0.4305567 0.718572
[,28] [,29] [,30] [,31] [,32] [,33] [,34]
[1,] -0.3931808 1.627342 1.098807 -0.6942009 -1.362404 -0.3044697 0.7167997
[2,] -0.3931808 1.627342 1.098807 -0.6942009 -1.362404 -0.3044697 0.7167997
[,35] [,36] [,37] [,38] [,39] [,40] [,41]
[1,] 0.3153664 0.1497402 1.416817 1.237428 1.020069 -0.812305 -1.446327
[2,] 0.3153664 0.1497402 1.416817 1.237428 1.020069 -0.812305 -1.446327
[,42] [,43] [,44] [,45] [,46] [,47] [,48]
[1,] 0.7824216 0.5327746 0.209389 1.014508 -0.4467246 -2.755298 -1.260761
[2,] 0.7824216 0.5327746 0.209389 1.014508 -0.4467246 -2.755298 -1.260761
[,49] [,50] [,51] [,52] [,53] [,54] [,55]
[1,] 0.8005478 1.297024 -1.107504 0.6169725 -0.1087848 0.08529164 0.2210026
[2,] 0.8005478 1.297024 -1.107504 0.6169725 -0.1087848 0.08529164 0.2210026
[,56] [,57] [,58] [,59] [,60] [,61] [,62]
[1,] 1.202381 -0.2197901 0.2017056 -0.4782316 0.2338867 -0.8920265 1.602039
[2,] 1.202381 -0.2197901 0.2017056 -0.4782316 0.2338867 -0.8920265 1.602039
[,63] [,64] [,65] [,66] [,67] [,68] [,69]
[1,] -1.43338 0.7820508 -1.050929 1.644877 -0.05254896 0.3779765 1.160539
[2,] -1.43338 0.7820508 -1.050929 1.644877 -0.05254896 0.3779765 1.160539
[,70] [,71] [,72] [,73] [,74] [,75] [,76]
[1,] -0.8296741 -0.887325 0.1408119 0.7913183 1.452982 0.3195446 -0.006583557
[2,] -0.8296741 -0.887325 0.1408119 0.7913183 1.452982 0.3195446 -0.006583557
[,77] [,78] [,79] [,80] [,81] [,82] [,83]
[1,] -1.975596 -0.4247838 -0.5539484 -0.6406027 -0.3582777 -0.9070397 0.7455244
[2,] -1.975596 -0.4247838 -0.5539484 -0.6406027 -0.3582777 -0.9070397 0.7455244
[,84] [,85] [,86] [,87] [,88] [,89] [,90]
[1,] -0.7843371 1.171893 -0.7521966 -1.360525 -0.9677405 -0.8347854 0.5936135
[2,] -0.7843371 1.171893 -0.7521966 -1.360525 -0.9677405 -0.8347854 0.5936135
[,91] [,92] [,93] [,94] [,95] [,96] [,97]
[1,] 1.782971 0.9881437 0.6117816 -1.007158 -0.2582788 0.8215907 -1.073862
[2,] 1.782971 0.9881437 0.6117816 -1.007158 -0.2582788 0.8215907 -1.073862
[,98] [,99] [,100]
[1,] -1.775418 -0.364612 -0.4960967
[2,] -1.775418 -0.364612 -0.4960967
>
>
> Max(tmp2)
[1] 2.885914
> Min(tmp2)
[1] -2.260292
> mean(tmp2)
[1] 0.02704815
> Sum(tmp2)
[1] 2.704815
> Var(tmp2)
[1] 0.984169
>
> rowMeans(tmp2)
[1] -0.86652979 -0.19939397 -0.35156979 1.10536843 -1.60793156 0.79350159
[7] -1.56672270 -0.92127242 0.41917891 0.25046045 -2.26029157 -0.30019386
[13] -0.48079646 -0.26477164 1.37388205 0.08343389 0.08295068 0.34332496
[19] -0.53895369 0.81316481 1.33416039 -1.48962198 -1.37112231 1.81943582
[25] 0.37680877 2.36577803 -0.37425641 -0.48403188 0.04449551 2.88591390
[31] 0.64477882 -1.74578015 0.77905903 0.79315381 0.30819632 -0.11343342
[37] 0.04376681 -0.78313814 0.67771460 0.11917895 0.09039577 -1.29612896
[43] -1.50358544 1.77327652 -0.17195575 0.40831143 0.35064769 -0.91356143
[49] -0.45555931 1.27131945 -0.23933662 0.71320998 -0.04835932 -0.50769378
[55] -0.41808118 0.74609268 -0.44676008 0.60370225 -0.43968808 -0.71916964
[61] 0.48824406 0.11038120 -0.49636216 0.19213322 -1.17618291 -0.14200088
[67] -0.47195732 0.37014378 2.34645921 2.22778744 2.30049572 -0.08968490
[73] -1.21362035 0.10887075 -1.06002750 -0.68851841 0.27282200 0.93554451
[79] 0.17363334 -0.49014239 -1.06553940 -0.90664936 -0.72017664 -0.82887144
[85] -1.72090881 0.54805289 0.08170598 0.27717729 -0.16071664 0.89606008
[91] 0.21367615 2.07124911 0.85464827 -0.06819565 0.43871788 -0.37729006
[97] -0.06446042 -0.04062405 -1.51118985 0.55516027
> rowSums(tmp2)
[1] -0.86652979 -0.19939397 -0.35156979 1.10536843 -1.60793156 0.79350159
[7] -1.56672270 -0.92127242 0.41917891 0.25046045 -2.26029157 -0.30019386
[13] -0.48079646 -0.26477164 1.37388205 0.08343389 0.08295068 0.34332496
[19] -0.53895369 0.81316481 1.33416039 -1.48962198 -1.37112231 1.81943582
[25] 0.37680877 2.36577803 -0.37425641 -0.48403188 0.04449551 2.88591390
[31] 0.64477882 -1.74578015 0.77905903 0.79315381 0.30819632 -0.11343342
[37] 0.04376681 -0.78313814 0.67771460 0.11917895 0.09039577 -1.29612896
[43] -1.50358544 1.77327652 -0.17195575 0.40831143 0.35064769 -0.91356143
[49] -0.45555931 1.27131945 -0.23933662 0.71320998 -0.04835932 -0.50769378
[55] -0.41808118 0.74609268 -0.44676008 0.60370225 -0.43968808 -0.71916964
[61] 0.48824406 0.11038120 -0.49636216 0.19213322 -1.17618291 -0.14200088
[67] -0.47195732 0.37014378 2.34645921 2.22778744 2.30049572 -0.08968490
[73] -1.21362035 0.10887075 -1.06002750 -0.68851841 0.27282200 0.93554451
[79] 0.17363334 -0.49014239 -1.06553940 -0.90664936 -0.72017664 -0.82887144
[85] -1.72090881 0.54805289 0.08170598 0.27717729 -0.16071664 0.89606008
[91] 0.21367615 2.07124911 0.85464827 -0.06819565 0.43871788 -0.37729006
[97] -0.06446042 -0.04062405 -1.51118985 0.55516027
> 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] -0.86652979 -0.19939397 -0.35156979 1.10536843 -1.60793156 0.79350159
[7] -1.56672270 -0.92127242 0.41917891 0.25046045 -2.26029157 -0.30019386
[13] -0.48079646 -0.26477164 1.37388205 0.08343389 0.08295068 0.34332496
[19] -0.53895369 0.81316481 1.33416039 -1.48962198 -1.37112231 1.81943582
[25] 0.37680877 2.36577803 -0.37425641 -0.48403188 0.04449551 2.88591390
[31] 0.64477882 -1.74578015 0.77905903 0.79315381 0.30819632 -0.11343342
[37] 0.04376681 -0.78313814 0.67771460 0.11917895 0.09039577 -1.29612896
[43] -1.50358544 1.77327652 -0.17195575 0.40831143 0.35064769 -0.91356143
[49] -0.45555931 1.27131945 -0.23933662 0.71320998 -0.04835932 -0.50769378
[55] -0.41808118 0.74609268 -0.44676008 0.60370225 -0.43968808 -0.71916964
[61] 0.48824406 0.11038120 -0.49636216 0.19213322 -1.17618291 -0.14200088
[67] -0.47195732 0.37014378 2.34645921 2.22778744 2.30049572 -0.08968490
[73] -1.21362035 0.10887075 -1.06002750 -0.68851841 0.27282200 0.93554451
[79] 0.17363334 -0.49014239 -1.06553940 -0.90664936 -0.72017664 -0.82887144
[85] -1.72090881 0.54805289 0.08170598 0.27717729 -0.16071664 0.89606008
[91] 0.21367615 2.07124911 0.85464827 -0.06819565 0.43871788 -0.37729006
[97] -0.06446042 -0.04062405 -1.51118985 0.55516027
> rowMin(tmp2)
[1] -0.86652979 -0.19939397 -0.35156979 1.10536843 -1.60793156 0.79350159
[7] -1.56672270 -0.92127242 0.41917891 0.25046045 -2.26029157 -0.30019386
[13] -0.48079646 -0.26477164 1.37388205 0.08343389 0.08295068 0.34332496
[19] -0.53895369 0.81316481 1.33416039 -1.48962198 -1.37112231 1.81943582
[25] 0.37680877 2.36577803 -0.37425641 -0.48403188 0.04449551 2.88591390
[31] 0.64477882 -1.74578015 0.77905903 0.79315381 0.30819632 -0.11343342
[37] 0.04376681 -0.78313814 0.67771460 0.11917895 0.09039577 -1.29612896
[43] -1.50358544 1.77327652 -0.17195575 0.40831143 0.35064769 -0.91356143
[49] -0.45555931 1.27131945 -0.23933662 0.71320998 -0.04835932 -0.50769378
[55] -0.41808118 0.74609268 -0.44676008 0.60370225 -0.43968808 -0.71916964
[61] 0.48824406 0.11038120 -0.49636216 0.19213322 -1.17618291 -0.14200088
[67] -0.47195732 0.37014378 2.34645921 2.22778744 2.30049572 -0.08968490
[73] -1.21362035 0.10887075 -1.06002750 -0.68851841 0.27282200 0.93554451
[79] 0.17363334 -0.49014239 -1.06553940 -0.90664936 -0.72017664 -0.82887144
[85] -1.72090881 0.54805289 0.08170598 0.27717729 -0.16071664 0.89606008
[91] 0.21367615 2.07124911 0.85464827 -0.06819565 0.43871788 -0.37729006
[97] -0.06446042 -0.04062405 -1.51118985 0.55516027
>
> colMeans(tmp2)
[1] 0.02704815
> colSums(tmp2)
[1] 2.704815
> colVars(tmp2)
[1] 0.984169
> colSd(tmp2)
[1] 0.9920529
> colMax(tmp2)
[1] 2.885914
> colMin(tmp2)
[1] -2.260292
> colMedians(tmp2)
[1] 0.001571379
> colRanges(tmp2)
[,1]
[1,] -2.260292
[2,] 2.885914
>
> dataset1 <- matrix(dataset1,1,100)
>
> agree.checks(tmp,dataset1)
>
> dataset2 <- matrix(dataset2,100,1)
> agree.checks(tmp2,dataset2)
>
>
> tmp <- createBufferedMatrix(10,10)
>
> tmp[1:10,1:10] <- rnorm(100)
> colApply(tmp,sum)
[1] -1.650992 -6.409317 0.351652 3.401025 -1.830937 5.512571 1.992616
[8] -4.511370 2.535593 -4.757825
> colApply(tmp,quantile)[,1]
[,1]
[1,] -2.57787291
[2,] -0.52791599
[3,] 0.04544668
[4,] 0.64426248
[5,] 0.76181382
>
> rowApply(tmp,sum)
[1] -2.72511135 4.40324013 1.18793617 -0.03955188 -0.89143087 -2.49220583
[7] 1.24317434 2.28692801 -3.04776561 -5.29219604
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 9 6 8 6 6 6 3 3 1 4
[2,] 4 5 5 1 4 7 6 5 3 2
[3,] 6 2 4 8 10 5 5 1 9 8
[4,] 10 8 9 2 5 4 7 2 10 7
[5,] 2 1 3 9 1 8 8 8 5 1
[6,] 3 7 6 7 2 9 10 10 6 10
[7,] 7 10 2 5 9 10 1 7 7 9
[8,] 5 3 7 3 8 2 2 4 8 3
[9,] 8 9 10 4 3 3 9 6 4 5
[10,] 1 4 1 10 7 1 4 9 2 6
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] 4.2998141 0.7231256 -1.0017189 -0.7778357 -0.9134230 1.6159984
[7] 0.5159809 -4.8023533 -0.8724229 -2.8445115 1.4652180 2.9563096
[13] -3.1594849 -1.2876238 2.5538119 2.0683489 -1.2701239 -1.3185071
[19] 2.2207584 3.0496394
> colApply(tmp,quantile)[,1]
[,1]
[1,] 0.05593308
[2,] 0.53314775
[3,] 0.82566233
[4,] 1.00418315
[5,] 1.88088775
>
> rowApply(tmp,sum)
[1] 2.5492199 -1.6550606 -2.6184377 4.2066283 0.7386501
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 17 20 17 9 16
[2,] 13 13 11 14 8
[3,] 10 4 16 4 7
[4,] 6 14 14 10 1
[5,] 14 7 6 1 20
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 1.00418315 0.55038695 -0.1037738 -0.17506822 0.5746188 -0.1093381
[2,] 1.88088775 -0.00170857 -0.8212211 0.05665711 -0.4587070 -2.1267460
[3,] 0.82566233 -0.03851542 0.8134437 0.47499233 -0.8173623 1.2809266
[4,] 0.05593308 0.47546679 -0.4948925 0.05604828 -1.6667869 2.3469753
[5,] 0.53314775 -0.26250412 -0.3952753 -1.19046517 1.4548144 0.2241806
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] 1.0845670 -2.1394355 0.4677592 -1.0617335 -0.1418965 1.5240371
[2,] 1.5399157 -1.0761596 -0.3371119 -1.8436258 0.9433071 0.4187592
[3,] -1.9110439 -2.2575339 -0.2109694 -0.8733145 1.2585679 -0.6892832
[4,] 0.5312417 1.1112885 -1.0974647 0.1390873 -1.0594541 1.1807743
[5,] -0.7286996 -0.4405129 0.3053638 0.7950750 0.4646935 0.5220222
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] -1.0179955 -0.6179428 2.098513776 -0.1599154 0.69323384 -1.0872174
[2,] -0.0262812 -0.6354778 -0.004720347 1.7383506 -0.80575674 0.5339843
[3,] -1.5194788 0.1061735 -0.153633812 1.4574499 -1.15421922 -0.1172364
[4,] 0.1357683 -0.1951498 0.065986424 -0.3416713 -0.02734249 -0.4658781
[5,] -0.7314976 0.0547731 0.547665895 -0.6258648 0.02396073 -0.1821595
[,19] [,20]
[1,] 0.6674009 0.4988359
[2,] -0.2904581 -0.3389483
[3,] 0.5893163 0.3176206
[4,] 2.1735034 1.2831948
[5,] -0.9190042 1.2889364
>
>
> 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 : 653 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 : 564 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 0.990979 -0.7717496 -1.333692 0.4839753 -0.4662082 -1.090387 -1.057408
col8 col9 col10 col11 col12 col13 col14
row1 0.3167697 -0.9099596 0.344666 -0.157478 0.6441953 1.217922 -0.7469432
col15 col16 col17 col18 col19 col20
row1 0.9835725 0.07990314 -1.850941 0.1227829 0.06754347 0.8887629
> tmp[,"col10"]
col10
row1 0.34466602
row2 0.04472475
row3 -0.85155464
row4 2.28937434
row5 -1.03634762
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7
row1 0.9909790 -0.7717496 -1.3336921 0.4839753 -0.4662082 -1.090387 -1.057408
row5 0.4042129 -0.8679418 -0.4151645 -0.1008312 -1.3279897 -1.120255 2.016811
col8 col9 col10 col11 col12 col13 col14
row1 0.31676975 -0.9099596 0.344666 -0.1574780 0.6441953 1.217922 -0.74694319
row5 0.03469156 -0.5152494 -1.036348 -0.1290717 -0.1381628 1.244206 0.01508384
col15 col16 col17 col18 col19 col20
row1 0.9835725 0.07990314 -1.850941 0.1227829 0.06754347 0.8887629
row5 -2.5526271 -0.05532250 -1.658956 -2.5938613 0.71700117 0.9192153
> tmp[,c("col6","col20")]
col6 col20
row1 -1.0903869 0.88876286
row2 0.3220865 0.07823971
row3 -0.3836280 -1.19813305
row4 1.9293844 -1.31088934
row5 -1.1202546 0.91921535
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 -1.090387 0.8887629
row5 -1.120255 0.9192153
>
>
>
>
> 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 50.51705 49.02864 48.22656 51.45379 51.00091 104.4554 51.01427 51.53185
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.123 50.39194 50.42272 50.75 51.25601 47.56292 47.55984 51.33814
col17 col18 col19 col20
row1 48.67024 49.33529 48.6919 105.6524
> tmp[,"col10"]
col10
row1 50.39194
row2 29.32153
row3 30.23966
row4 30.27665
row5 49.18938
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 50.51705 49.02864 48.22656 51.45379 51.00091 104.4554 51.01427 51.53185
row5 51.14676 49.07602 50.27156 49.51110 48.24730 104.9878 49.14758 48.94561
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.12300 50.39194 50.42272 50.750 51.25601 47.56292 47.55984 51.33814
row5 50.87215 49.18938 51.52485 48.697 48.95898 49.69292 48.86219 49.74198
col17 col18 col19 col20
row1 48.67024 49.33529 48.69190 105.6524
row5 49.27621 50.73549 49.82794 104.7929
> tmp[,c("col6","col20")]
col6 col20
row1 104.45537 105.65244
row2 75.68824 73.89115
row3 74.73540 73.50788
row4 75.41711 74.77943
row5 104.98782 104.79291
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 104.4554 105.6524
row5 104.9878 104.7929
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 104.4554 105.6524
row5 104.9878 104.7929
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] 1.5580970
[2,] 0.5815942
[3,] 1.4066527
[4,] -1.0118597
[5,] 0.4844747
> tmp[,c("col17","col7")]
col17 col7
[1,] -0.6837960 0.04702717
[2,] -0.6338772 0.82667476
[3,] 0.1619223 -1.18382817
[4,] -0.6716295 1.19917223
[5,] 0.9751022 1.04865298
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] 0.15065230 0.1784371
[2,] -0.05483568 -1.5837145
[3,] -0.11245724 0.9515241
[4,] 0.83038256 -1.1494677
[5,] -0.13364260 0.3383250
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] 0.1506523
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] 0.15065230
[2,] -0.05483568
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
>
>
>
> subBufferedMatrix(tmp,c("row3","row1"),)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6]
row3 -1.9706815 0.9452341 -0.5093532 -0.8462124 0.7849055 -1.5945579
row1 0.3892537 -1.5553436 -1.4313044 -0.1010384 0.6268318 0.9895162
[,7] [,8] [,9] [,10] [,11] [,12] [,13]
row3 -0.6166020 0.1518291 -0.3423721 0.9040989 1.3749407 -0.6127882 0.7305387
row1 -0.2399155 0.6113007 0.3150543 -0.6843601 -0.8610598 -0.6346585 0.3923657
[,14] [,15] [,16] [,17] [,18] [,19]
row3 0.4674693 -2.30159453 1.4230633 -0.98668874 0.6037258 0.7275143
row1 1.5073710 -0.01368708 -0.9234298 0.03825243 -1.5999940 0.5684518
[,20]
row3 0.5835052
row1 -1.5532585
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 0.07846426 0.02188932 0.3742646 0.1877484 -0.5864625 1.313709 -0.3758374
[,8] [,9] [,10]
row2 0.2646305 -1.379308 -0.1278019
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 -1.226102 -0.8408383 -1.124326 0.2739234 1.005596 2.617431 -0.1489066
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 -1.065641 1.534591 0.8347799 0.9186488 0.9924576 0.09158194 0.7185536
[,15] [,16] [,17] [,18] [,19] [,20]
row5 -0.3922812 0.4258018 -0.8737428 -0.4681296 0.5625765 0.33691
>
>
> 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: 0x58f9a8f32b20>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM15894d53d82610"
[2] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM15894d13ab0756"
[3] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM15894d4fe2e2bd"
[4] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM15894d49a20085"
[5] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM15894d707cf665"
[6] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM15894d4f05fc10"
[7] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM15894d3ae106b"
[8] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM15894d27795ed"
[9] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM15894dc89b204"
[10] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM15894d642f042f"
[11] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM15894d6d3da3c0"
[12] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM15894d5d09490a"
[13] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM15894dd322065"
[14] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM15894d1e9a2ee7"
[15] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM15894d1623a6d4"
>
>
> ### 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: 0x58f9aa8a9b80>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x58f9aa8a9b80>
Warning message:
In dir.create(new.directory) :
'/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x58f9aa8a9b80>
> rowMedians(tmp)
[1] 0.306052264 -0.174938936 0.384492980 0.288768811 0.549617090
[6] 0.045752153 -0.362890660 0.326744071 0.020884044 0.283386725
[11] -0.456859817 0.098031472 -0.237290107 0.239587649 0.027488603
[16] 0.225847178 -0.065429223 -0.228380004 -0.145398609 0.361712841
[21] -0.289536512 0.008277605 0.621322001 0.684824162 -0.623430672
[26] -0.278238958 0.811232646 -0.420159049 -0.192392609 -0.161706615
[31] 0.071438262 0.506129053 0.077390214 -0.361078549 -0.131923638
[36] -0.006159395 -0.015856448 -0.008574215 -0.350587840 0.320764975
[41] -0.275848075 -0.035340522 0.078628871 -0.607285767 -0.231036481
[46] -0.195847718 0.108834576 -0.426281072 -0.630802123 -0.553842812
[51] -0.748647989 -0.057006836 -0.754957363 -0.260054073 -0.170202877
[56] -0.268159097 -0.196103292 -0.214281316 -0.110618390 0.024862664
[61] 0.117355742 -0.258554249 -0.101802573 -0.488929524 0.102471742
[66] -0.472986950 0.024827599 0.089793553 0.187606259 -0.102961919
[71] 0.351492843 0.132056750 -0.208912873 0.410877159 0.295938476
[76] 0.160576766 -0.272998514 0.145134721 -0.108764156 0.297942458
[81] 0.603519909 -0.205740345 -0.034326110 -0.107723788 -0.136854881
[86] -0.165415591 0.126065900 -0.009371902 -0.577990210 -0.424726443
[91] 0.020515076 0.245261183 0.416679490 -0.289533739 -0.583652821
[96] -0.087301180 0.158917341 0.216117186 -0.278364838 0.077029960
[101] -0.268829250 0.432713778 -0.311349565 0.429961945 0.221675858
[106] 0.324944720 -0.332198263 -0.186491622 0.128445482 -0.454455329
[111] -0.114807367 -0.333253190 0.484978054 -0.386168779 -0.182078693
[116] -0.126796387 -0.153448648 -0.107175363 0.173455549 0.594379539
[121] -0.023197064 0.005363949 -0.314543116 -0.526069715 0.396200983
[126] 0.239927572 0.063965617 0.129585946 0.058605452 0.539474814
[131] 0.055116558 -0.115350390 -0.457347345 -0.041723676 0.213810566
[136] -0.082994588 0.020300241 0.567298363 -0.023313783 -0.224944655
[141] 0.201800665 -0.066487041 -0.002388045 0.147908752 0.201462704
[146] 0.230795859 -0.092266867 -0.373617441 -0.190237235 -0.402861554
[151] 0.049693051 -0.446808621 0.042188209 0.086029048 -0.143881233
[156] -0.252322979 -0.539524713 0.112504903 0.225038015 0.001192867
[161] 0.404497394 0.282804590 0.083716991 -0.475908567 -0.048667249
[166] -0.429475700 -0.031204137 -0.349831460 0.184178688 0.224460295
[171] -0.087801783 0.433013625 0.563085069 0.020706395 -0.338694730
[176] 0.463647786 0.211736888 -0.153782750 0.073031605 0.163651994
[181] 0.059123761 0.219159456 0.185475451 0.036719417 -0.014668997
[186] 0.002913037 0.308743555 -0.242750075 0.238361363 -0.400768106
[191] -0.457756470 -0.288460247 -0.184208455 0.525012573 -0.646062976
[196] 0.492132435 0.118237838 0.242096910 -0.463636214 -0.070199617
[201] 0.415958570 -0.140606588 0.117063901 0.247895778 0.027575252
[206] 0.541889230 -0.429587205 0.029616722 -0.440825180 0.460378220
[211] -0.089545051 -0.196584600 0.127724154 -0.436311402 -0.419908733
[216] -0.086524378 -0.125066107 -0.477445979 -0.033003448 0.089458051
[221] -0.048391852 0.083897923 0.190516517 -0.115054296 -0.023170701
[226] 0.533665434 -0.261104539 0.458849592 0.289809919 -0.489238883
>
> proc.time()
user system elapsed
1.294 0.661 1.943
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: 0x55c3625f11c0>
> .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: 0x55c3625f11c0>
> .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: 0x55c3625f11c0>
> .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: 0x55c3625f11c0>
> 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: 0x55c3628d4120>
> .Call("R_bm_AddColumn",P)
<pointer: 0x55c3628d4120>
> .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: 0x55c3628d4120>
> .Call("R_bm_AddColumn",P)
<pointer: 0x55c3628d4120>
> .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: 0x55c3628d4120>
> 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: 0x55c3615884a0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x55c3615884a0>
> .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: 0x55c3615884a0>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x55c3615884a0>
> .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: 0x55c3615884a0>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x55c3615884a0>
> .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: 0x55c3615884a0>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x55c3615884a0>
> .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: 0x55c3615884a0>
> 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: 0x55c361624390>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x55c361624390>
> .Call("R_bm_AddColumn",P)
<pointer: 0x55c361624390>
> .Call("R_bm_AddColumn",P)
<pointer: 0x55c361624390>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile158b01284ff039" "BufferedMatrixFile158b01ae5f110"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile158b01284ff039" "BufferedMatrixFile158b01ae5f110"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x55c361ea3650>
> .Call("R_bm_AddColumn",P)
<pointer: 0x55c361ea3650>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x55c361ea3650>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x55c361ea3650>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x55c361ea3650>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x55c361ea3650>
> .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: 0x55c36302a430>
> .Call("R_bm_AddColumn",P)
<pointer: 0x55c36302a430>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x55c36302a430>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x55c36302a430>
> 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: 0x55c36331f250>
> .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: 0x55c36331f250>
> rm(P)
>
> proc.time()
user system elapsed
0.240 0.049 0.277
BufferedMatrix.Rcheck/tests/Rcodetesting.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
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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
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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
0.272 0.041 0.302