Ben Bolstad
| Snapshot Date: 2026-03-27 13:45 -0400 (Fri, 27 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 2026-03-28 11:57 -0400 (Sat, 28 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: 2026-03-27 21:31:50 -0400 (Fri, 27 Mar 2026) |
| EndedAt: 2026-03-27 21:32:14 -0400 (Fri, 27 Mar 2026) |
| EllapsedTime: 24.1 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
0.234 0.052 0.276
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] "Fri Mar 27 21:32:05 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] "Fri Mar 27 21:32:05 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: 0x65148e8dc370>
>
>
>
> 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] "Fri Mar 27 21:32:05 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] "Fri Mar 27 21:32:05 2026"
>
> ColMode(tmp2)
<pointer: 0x65148e8dc370>
>
>
>
> ### Now testing assignments
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+
+ new.data <- rnorm(20)
+ tmp2[which.row,] <- new.data
+ test.matrix[which.row,] <- new.data
+ if (rep > 1){
+ if (!all(tmp2[prev.row,] == test.matrix[prev.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ new.data <- rnorm(10)
+ tmp2[,which.col] <- new.data
+ test.matrix[,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[,prev.col] == test.matrix[,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.col <- which.col
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,5,replace=TRUE)
+ new.data <- matrix(rnorm(50),5,10)
+ tmp2[,which.col] <- new.data
+ test.matrix[,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[,prev.col] == test.matrix[,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.col <- which.col
+ }
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ new.data <- matrix(rnorm(50),5,10)
+ tmp2[which.row,] <- new.data
+ test.matrix[which.row,]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[prev.row,] == test.matrix[prev.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:20,5,replace=TRUE)
+ new.data <- matrix(rnorm(25),5,5)
+ tmp2[which.row,which.col] <- new.data
+ test.matrix[which.row,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[prev.row,prev.col] == test.matrix[prev.row,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+ prev.col <- which.col
+ }
>
>
>
>
> ###
> ###
> ### testing some more functions
> ###
>
>
>
> ## duplication function
> tmp5 <- duplicate(tmp2)
>
> # making sure really did copy everything.
> tmp5[1,1] <- tmp5[1,1] +100.00
>
> if (tmp5[1,1] == tmp2[1,1]){
+ stop("Problem with duplication")
+ }
>
>
>
>
> ### testing elementwise applying of functions
>
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 100.142128370 -0.2442367 1.4269976 0.9731212
[2,] -0.008531264 0.9370174 0.7328607 -0.5571028
[3,] 0.623540346 0.5224237 -0.8844896 1.2341850
[4,] -0.954542959 0.4621154 -1.8932767 -1.0290733
> 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,] 1.001421e+02 0.2442367 1.4269976 0.9731212
[2,] 8.531264e-03 0.9370174 0.7328607 0.5571028
[3,] 6.235403e-01 0.5224237 0.8844896 1.2341850
[4,] 9.545430e-01 0.4621154 1.8932767 1.0290733
> ewApply(tmp5,sqrt)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 2 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 10.00710390 0.4942031 1.1945701 0.9864691
[2,] 0.09236484 0.9679966 0.8560728 0.7463932
[3,] 0.78964571 0.7227888 0.9404731 1.1109388
[4,] 0.97700714 0.6797907 1.3759639 1.0144325
>
> my.function <- function(x,power){
+ (x+5)^power
+ }
>
> ewApply(tmp5,my.function,power=2)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 2 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 225.21317 30.18627 38.37270 35.83781
[2,] 25.93218 35.61698 34.29359 33.02103
[3,] 33.52000 32.75031 35.28922 37.34357
[4,] 35.72461 32.26002 40.65292 36.17340
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x65148f8d89b0>
> exp(tmp5)
<pointer: 0x65148f8d89b0>
> log(tmp5,2)
<pointer: 0x65148f8d89b0>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 468.7517
> Min(tmp5)
[1] 53.97443
> mean(tmp5)
[1] 73.55218
> Sum(tmp5)
[1] 14710.44
> Var(tmp5)
[1] 855.419
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 89.69549 72.49293 70.88226 73.82246 70.69597 69.96272 70.44029 73.77070
[9] 72.66705 71.09192
> rowSums(tmp5)
[1] 1793.910 1449.859 1417.645 1476.449 1413.919 1399.254 1408.806 1475.414
[9] 1453.341 1421.838
> rowVars(tmp5)
[1] 7997.62442 106.92102 60.22842 81.31126 55.83064 38.19523
[7] 57.55854 86.12277 67.77258 85.14965
> rowSd(tmp5)
[1] 89.429438 10.340262 7.760697 9.017276 7.471990 6.180229 7.586734
[8] 9.280235 8.232410 9.227657
> rowMax(tmp5)
[1] 468.75170 98.90580 85.98103 86.17438 91.65694 81.47855 85.40884
[8] 89.95685 86.34091 89.52047
> rowMin(tmp5)
[1] 60.55036 53.97443 58.12235 59.66490 60.75267 57.74806 59.08183 58.84203
[9] 57.95196 57.01475
>
> colMeans(tmp5)
[1] 108.09305 71.37566 73.88774 74.84185 72.39421 70.62815 69.20956
[8] 74.07320 73.78712 67.60172 69.25495 76.52801 72.22679 67.42705
[15] 70.26525 70.25628 70.83159 69.98283 75.04044 73.33812
> colSums(tmp5)
[1] 1080.9305 713.7566 738.8774 748.4185 723.9421 706.2815 692.0956
[8] 740.7320 737.8712 676.0172 692.5495 765.2801 722.2679 674.2705
[15] 702.6525 702.5628 708.3159 699.8283 750.4044 733.3812
> colVars(tmp5)
[1] 16105.12948 28.25274 84.14010 43.41611 91.44933 55.96172
[7] 33.25430 74.59021 91.02012 18.57274 50.08798 127.17324
[13] 42.19491 60.65884 59.69077 101.50051 63.56791 46.11011
[19] 114.82364 95.18765
> colSd(tmp5)
[1] 126.905987 5.315331 9.172791 6.589090 9.562914 7.480756
[7] 5.766654 8.636562 9.540447 4.309610 7.077286 11.277111
[13] 6.495761 7.788379 7.725980 10.074746 7.972948 6.790443
[19] 10.715579 9.756416
> colMax(tmp5)
[1] 468.75170 82.73717 89.06455 85.89600 85.77003 84.82027 76.17710
[8] 86.17438 88.03391 74.89511 85.98678 98.90580 84.01077 85.40884
[15] 86.34091 89.27261 85.98103 81.46489 89.95685 91.65694
> colMin(tmp5)
[1] 53.97443 62.82876 61.80804 62.67084 57.74806 62.19543 57.01475 58.70238
[9] 57.95196 61.93243 61.65540 59.54353 62.69828 56.76077 60.55036 58.66238
[17] 60.75267 59.08183 58.12235 58.84203
>
>
> ### setting a random element to NA and then testing with na.rm=TRUE or na.rm=FALSE (The default)
>
>
> which.row <- sample(1:10,1,replace=TRUE)
> which.col <- sample(1:20,1,replace=TRUE)
>
> tmp5[which.row,which.col] <- NA
>
> Max(tmp5)
[1] NA
> Min(tmp5)
[1] NA
> mean(tmp5)
[1] NA
> Sum(tmp5)
[1] NA
> Var(tmp5)
[1] NA
>
> rowMeans(tmp5)
[1] 89.69549 72.49293 70.88226 73.82246 70.69597 69.96272 NA 73.77070
[9] 72.66705 71.09192
> rowSums(tmp5)
[1] 1793.910 1449.859 1417.645 1476.449 1413.919 1399.254 NA 1475.414
[9] 1453.341 1421.838
> rowVars(tmp5)
[1] 7997.62442 106.92102 60.22842 81.31126 55.83064 38.19523
[7] 50.44962 86.12277 67.77258 85.14965
> rowSd(tmp5)
[1] 89.429438 10.340262 7.760697 9.017276 7.471990 6.180229 7.102790
[8] 9.280235 8.232410 9.227657
> rowMax(tmp5)
[1] 468.75170 98.90580 85.98103 86.17438 91.65694 81.47855 NA
[8] 89.95685 86.34091 89.52047
> rowMin(tmp5)
[1] 60.55036 53.97443 58.12235 59.66490 60.75267 57.74806 NA 58.84203
[9] 57.95196 57.01475
>
> colMeans(tmp5)
[1] 108.09305 71.37566 73.88774 74.84185 72.39421 70.62815 69.20956
[8] 74.07320 73.78712 67.60172 69.25495 NA 72.22679 67.42705
[15] 70.26525 70.25628 70.83159 69.98283 75.04044 73.33812
> colSums(tmp5)
[1] 1080.9305 713.7566 738.8774 748.4185 723.9421 706.2815 692.0956
[8] 740.7320 737.8712 676.0172 692.5495 NA 722.2679 674.2705
[15] 702.6525 702.5628 708.3159 699.8283 750.4044 733.3812
> colVars(tmp5)
[1] 16105.12948 28.25274 84.14010 43.41611 91.44933 55.96172
[7] 33.25430 74.59021 91.02012 18.57274 50.08798 NA
[13] 42.19491 60.65884 59.69077 101.50051 63.56791 46.11011
[19] 114.82364 95.18765
> colSd(tmp5)
[1] 126.905987 5.315331 9.172791 6.589090 9.562914 7.480756
[7] 5.766654 8.636562 9.540447 4.309610 7.077286 NA
[13] 6.495761 7.788379 7.725980 10.074746 7.972948 6.790443
[19] 10.715579 9.756416
> colMax(tmp5)
[1] 468.75170 82.73717 89.06455 85.89600 85.77003 84.82027 76.17710
[8] 86.17438 88.03391 74.89511 85.98678 NA 84.01077 85.40884
[15] 86.34091 89.27261 85.98103 81.46489 89.95685 91.65694
> colMin(tmp5)
[1] 53.97443 62.82876 61.80804 62.67084 57.74806 62.19543 57.01475 58.70238
[9] 57.95196 61.93243 61.65540 NA 62.69828 56.76077 60.55036 58.66238
[17] 60.75267 59.08183 58.12235 58.84203
>
> Max(tmp5,na.rm=TRUE)
[1] 468.7517
> Min(tmp5,na.rm=TRUE)
[1] 53.97443
> mean(tmp5,na.rm=TRUE)
[1] 73.5011
> Sum(tmp5,na.rm=TRUE)
[1] 14626.72
> Var(tmp5,na.rm=TRUE)
[1] 859.2149
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 89.69549 72.49293 70.88226 73.82246 70.69597 69.96272 69.74157 73.77070
[9] 72.66705 71.09192
> rowSums(tmp5,na.rm=TRUE)
[1] 1793.910 1449.859 1417.645 1476.449 1413.919 1399.254 1325.090 1475.414
[9] 1453.341 1421.838
> rowVars(tmp5,na.rm=TRUE)
[1] 7997.62442 106.92102 60.22842 81.31126 55.83064 38.19523
[7] 50.44962 86.12277 67.77258 85.14965
> rowSd(tmp5,na.rm=TRUE)
[1] 89.429438 10.340262 7.760697 9.017276 7.471990 6.180229 7.102790
[8] 9.280235 8.232410 9.227657
> rowMax(tmp5,na.rm=TRUE)
[1] 468.75170 98.90580 85.98103 86.17438 91.65694 81.47855 85.40884
[8] 89.95685 86.34091 89.52047
> rowMin(tmp5,na.rm=TRUE)
[1] 60.55036 53.97443 58.12235 59.66490 60.75267 57.74806 59.08183 58.84203
[9] 57.95196 57.01475
>
> colMeans(tmp5,na.rm=TRUE)
[1] 108.09305 71.37566 73.88774 74.84185 72.39421 70.62815 69.20956
[8] 74.07320 73.78712 67.60172 69.25495 75.72935 72.22679 67.42705
[15] 70.26525 70.25628 70.83159 69.98283 75.04044 73.33812
> colSums(tmp5,na.rm=TRUE)
[1] 1080.9305 713.7566 738.8774 748.4185 723.9421 706.2815 692.0956
[8] 740.7320 737.8712 676.0172 692.5495 681.5641 722.2679 674.2705
[15] 702.6525 702.5628 708.3159 699.8283 750.4044 733.3812
> colVars(tmp5,na.rm=TRUE)
[1] 16105.12948 28.25274 84.14010 43.41611 91.44933 55.96172
[7] 33.25430 74.59021 91.02012 18.57274 50.08798 135.89399
[13] 42.19491 60.65884 59.69077 101.50051 63.56791 46.11011
[19] 114.82364 95.18765
> colSd(tmp5,na.rm=TRUE)
[1] 126.905987 5.315331 9.172791 6.589090 9.562914 7.480756
[7] 5.766654 8.636562 9.540447 4.309610 7.077286 11.657358
[13] 6.495761 7.788379 7.725980 10.074746 7.972948 6.790443
[19] 10.715579 9.756416
> colMax(tmp5,na.rm=TRUE)
[1] 468.75170 82.73717 89.06455 85.89600 85.77003 84.82027 76.17710
[8] 86.17438 88.03391 74.89511 85.98678 98.90580 84.01077 85.40884
[15] 86.34091 89.27261 85.98103 81.46489 89.95685 91.65694
> colMin(tmp5,na.rm=TRUE)
[1] 53.97443 62.82876 61.80804 62.67084 57.74806 62.19543 57.01475 58.70238
[9] 57.95196 61.93243 61.65540 59.54353 62.69828 56.76077 60.55036 58.66238
[17] 60.75267 59.08183 58.12235 58.84203
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 89.69549 72.49293 70.88226 73.82246 70.69597 69.96272 NaN 73.77070
[9] 72.66705 71.09192
> rowSums(tmp5,na.rm=TRUE)
[1] 1793.910 1449.859 1417.645 1476.449 1413.919 1399.254 0.000 1475.414
[9] 1453.341 1421.838
> rowVars(tmp5,na.rm=TRUE)
[1] 7997.62442 106.92102 60.22842 81.31126 55.83064 38.19523
[7] NA 86.12277 67.77258 85.14965
> rowSd(tmp5,na.rm=TRUE)
[1] 89.429438 10.340262 7.760697 9.017276 7.471990 6.180229 NA
[8] 9.280235 8.232410 9.227657
> rowMax(tmp5,na.rm=TRUE)
[1] 468.75170 98.90580 85.98103 86.17438 91.65694 81.47855 NA
[8] 89.95685 86.34091 89.52047
> rowMin(tmp5,na.rm=TRUE)
[1] 60.55036 53.97443 58.12235 59.66490 60.75267 57.74806 NA 58.84203
[9] 57.95196 57.01475
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 112.75998 70.11327 73.27414 75.22008 72.84819 71.56512 69.09975
[8] 74.26834 73.99853 67.88574 69.80457 NaN 72.48916 65.42907
[15] 71.12978 69.94120 70.53431 71.19405 76.19960 74.47465
> colSums(tmp5,na.rm=TRUE)
[1] 1014.8398 631.0194 659.4673 676.9807 655.6337 644.0861 621.8977
[8] 668.4151 665.9868 610.9716 628.2411 0.0000 652.4024 588.8617
[15] 640.1680 629.4708 634.8088 640.7465 685.7964 670.2718
> colVars(tmp5,na.rm=TRUE)
[1] 17873.24304 13.85602 90.42190 47.23373 100.56188 53.08045
[7] 37.27543 83.48559 101.89485 19.98687 52.95060 NA
[13] 46.69483 23.33218 58.74373 113.07127 70.51971 35.36945
[19] 114.06046 92.55460
> colSd(tmp5,na.rm=TRUE)
[1] 133.690849 3.722368 9.509043 6.872680 10.028055 7.285633
[7] 6.105361 9.137045 10.094298 4.470668 7.276716 NA
[13] 6.833362 4.830340 7.664446 10.633498 8.397601 5.947222
[19] 10.679909 9.620530
> colMax(tmp5,na.rm=TRUE)
[1] 468.75170 74.16529 89.06455 85.89600 85.77003 84.82027 76.17710
[8] 86.17438 88.03391 74.89511 85.98678 -Inf 84.01077 72.44649
[15] 86.34091 89.27261 85.98103 81.46489 89.95685 91.65694
> colMin(tmp5,na.rm=TRUE)
[1] 53.97443 62.82876 61.80804 62.67084 57.74806 64.51943 57.01475 58.70238
[9] 57.95196 61.93243 61.65540 Inf 62.69828 56.76077 60.55036 58.66238
[17] 60.75267 61.85874 58.12235 58.84203
>
>
>
>
> 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] 213.5408 202.9587 209.3224 204.2855 168.2786 262.1138 396.6581 340.8313
[9] 171.7586 195.1099
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 213.5408 202.9587 209.3224 204.2855 168.2786 262.1138 396.6581 340.8313
[9] 171.7586 195.1099
>
>
>
> 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] -2.842171e-13 -1.989520e-13 5.684342e-14 2.842171e-14 -8.526513e-14
[6] 8.526513e-14 -7.105427e-14 0.000000e+00 0.000000e+00 5.684342e-14
[11] 1.421085e-13 2.842171e-14 -1.136868e-13 3.694822e-13 -1.136868e-13
[16] 1.136868e-13 -1.136868e-13 -1.136868e-13 5.684342e-14 3.979039e-13
>
>
>
>
>
>
>
>
>
>
> ## making sure these things agree
> ##
> ## first when there is no NA
>
>
>
> agree.checks <- function(buff.matrix,r.matrix,err.tol=1e-10){
+
+ if (Max(buff.matrix,na.rm=TRUE) != max(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Max")
+ }
+
+
+ if (Min(buff.matrix,na.rm=TRUE) != min(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Min")
+ }
+
+
+ if (abs(Sum(buff.matrix,na.rm=TRUE)- sum(r.matrix,na.rm=TRUE)) > err.tol){
+
+ cat(Sum(buff.matrix,na.rm=TRUE),"\n")
+ cat(sum(r.matrix,na.rm=TRUE),"\n")
+ cat(Sum(buff.matrix,na.rm=TRUE) - sum(r.matrix,na.rm=TRUE),"\n")
+
+ stop("No agreement in Sum")
+ }
+
+ if (abs(mean(buff.matrix,na.rm=TRUE) - mean(r.matrix,na.rm=TRUE)) > err.tol){
+ stop("No agreement in mean")
+ }
+
+
+ if(abs(Var(buff.matrix,na.rm=TRUE) - var(as.vector(r.matrix),na.rm=TRUE)) > err.tol){
+ stop("No agreement in Var")
+ }
+
+
+
+ if(any(abs(rowMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,mean,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowMeans")
+ }
+
+
+ if(any(abs(colMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,mean,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colMeans")
+ }
+
+
+ if(any(abs(rowSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in rowSums")
+ }
+
+
+ if(any(abs(colSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colSums")
+ }
+
+ ### this is to get around the fact that R doesn't like to compute NA on an entire vector of NA when
+ ### computing variance
+ my.Var <- function(x,na.rm=FALSE){
+ if (all(is.na(x))){
+ return(NA)
+ } else {
+ var(x,na.rm=na.rm)
+ }
+
+ }
+
+ if(any(abs(rowVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(colVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(rowMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+ if(any(abs(colMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+
+ if(any(abs(rowMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+
+ if(any(abs(colMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+ if(any(abs(colMedians(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,median,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMedian")
+ }
+
+ if(any(abs(colRanges(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,range,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colRanges")
+ }
+
+
+
+ }
>
>
>
>
>
>
>
>
>
> for (rep in 1:20){
+ copymatrix <- matrix(rnorm(200,150,15),10,20)
+
+ tmp5[1:10,1:20] <- copymatrix
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ## now lets assign some NA values and check agreement
+
+ which.row <- sample(1:10,1,replace=TRUE)
+ which.col <- sample(1:20,1,replace=TRUE)
+
+ cat(which.row," ",which.col,"\n")
+
+ tmp5[which.row,which.col] <- NA
+ copymatrix[which.row,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ## make an entire row NA
+ tmp5[which.row,] <- NA
+ copymatrix[which.row,] <- NA
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ### also make an entire col NA
+ tmp5[,which.col] <- NA
+ copymatrix[,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ### now make 1 element non NA with NA in the rest of row and column
+
+ tmp5[which.row,which.col] <- rnorm(1,150,15)
+ copymatrix[which.row,which.col] <- tmp5[which.row,which.col]
+
+ agree.checks(tmp5,copymatrix)
+ }
10 11
7 3
1 7
4 17
6 18
1 3
4 8
8 18
5 5
5 1
9 3
5 15
7 15
3 7
6 2
8 13
6 20
4 11
2 4
8 6
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] 2.935885
> Min(tmp)
[1] -2.839439
> mean(tmp)
[1] -0.130311
> Sum(tmp)
[1] -13.0311
> Var(tmp)
[1] 1.271724
>
> rowMeans(tmp)
[1] -0.130311
> rowSums(tmp)
[1] -13.0311
> rowVars(tmp)
[1] 1.271724
> rowSd(tmp)
[1] 1.127707
> rowMax(tmp)
[1] 2.935885
> rowMin(tmp)
[1] -2.839439
>
> colMeans(tmp)
[1] 1.224332013 -1.048779693 0.685835383 -0.027251408 -1.228547516
[6] -0.300622584 0.272407136 -0.755581494 0.077293788 -0.434769064
[11] -1.539016737 1.460704352 -0.973724781 0.965343333 -1.905663846
[16] -0.836053177 -0.148991142 -0.869913438 1.402276665 -1.547380001
[21] -0.631206211 1.592475825 0.029519451 1.002483237 -2.839438775
[26] 1.097318980 -0.137893350 2.935884988 -0.012061189 0.331061045
[31] 0.542748709 0.312860045 2.354616384 0.447634843 -1.909348008
[36] 0.250222220 0.475458107 0.162789723 -1.462369819 -1.969822606
[41] -0.081645611 -0.626761054 1.510348966 0.488548010 0.217891024
[46] 0.883408682 0.205482100 -1.833090844 -0.360412601 -1.322424259
[51] -0.179567832 0.727090127 1.265254006 -2.196918183 -0.020940069
[56] 0.501663551 -1.217610625 0.360446305 0.230213164 0.603788662
[61] 1.114155970 -0.003230589 -0.487628051 -0.890199831 1.931259665
[66] -0.387791754 0.062254225 0.873104942 -0.249700117 0.332699102
[71] -0.139818719 -1.891135351 -2.131477696 0.825593104 0.303848440
[76] -0.593174334 -0.192954039 1.279718511 0.618252600 -0.519520224
[81] -2.727924893 -0.023162340 -2.233303638 2.077439245 0.598040909
[86] -0.937305905 0.648613976 -0.147604962 -0.001565387 0.946162595
[91] -0.089111809 -0.040589582 -1.599463870 -0.223422338 -0.246624868
[96] -1.103711548 -1.846408658 -0.185648854 0.170592953 -2.119948650
> colSums(tmp)
[1] 1.224332013 -1.048779693 0.685835383 -0.027251408 -1.228547516
[6] -0.300622584 0.272407136 -0.755581494 0.077293788 -0.434769064
[11] -1.539016737 1.460704352 -0.973724781 0.965343333 -1.905663846
[16] -0.836053177 -0.148991142 -0.869913438 1.402276665 -1.547380001
[21] -0.631206211 1.592475825 0.029519451 1.002483237 -2.839438775
[26] 1.097318980 -0.137893350 2.935884988 -0.012061189 0.331061045
[31] 0.542748709 0.312860045 2.354616384 0.447634843 -1.909348008
[36] 0.250222220 0.475458107 0.162789723 -1.462369819 -1.969822606
[41] -0.081645611 -0.626761054 1.510348966 0.488548010 0.217891024
[46] 0.883408682 0.205482100 -1.833090844 -0.360412601 -1.322424259
[51] -0.179567832 0.727090127 1.265254006 -2.196918183 -0.020940069
[56] 0.501663551 -1.217610625 0.360446305 0.230213164 0.603788662
[61] 1.114155970 -0.003230589 -0.487628051 -0.890199831 1.931259665
[66] -0.387791754 0.062254225 0.873104942 -0.249700117 0.332699102
[71] -0.139818719 -1.891135351 -2.131477696 0.825593104 0.303848440
[76] -0.593174334 -0.192954039 1.279718511 0.618252600 -0.519520224
[81] -2.727924893 -0.023162340 -2.233303638 2.077439245 0.598040909
[86] -0.937305905 0.648613976 -0.147604962 -0.001565387 0.946162595
[91] -0.089111809 -0.040589582 -1.599463870 -0.223422338 -0.246624868
[96] -1.103711548 -1.846408658 -0.185648854 0.170592953 -2.119948650
> 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] 1.224332013 -1.048779693 0.685835383 -0.027251408 -1.228547516
[6] -0.300622584 0.272407136 -0.755581494 0.077293788 -0.434769064
[11] -1.539016737 1.460704352 -0.973724781 0.965343333 -1.905663846
[16] -0.836053177 -0.148991142 -0.869913438 1.402276665 -1.547380001
[21] -0.631206211 1.592475825 0.029519451 1.002483237 -2.839438775
[26] 1.097318980 -0.137893350 2.935884988 -0.012061189 0.331061045
[31] 0.542748709 0.312860045 2.354616384 0.447634843 -1.909348008
[36] 0.250222220 0.475458107 0.162789723 -1.462369819 -1.969822606
[41] -0.081645611 -0.626761054 1.510348966 0.488548010 0.217891024
[46] 0.883408682 0.205482100 -1.833090844 -0.360412601 -1.322424259
[51] -0.179567832 0.727090127 1.265254006 -2.196918183 -0.020940069
[56] 0.501663551 -1.217610625 0.360446305 0.230213164 0.603788662
[61] 1.114155970 -0.003230589 -0.487628051 -0.890199831 1.931259665
[66] -0.387791754 0.062254225 0.873104942 -0.249700117 0.332699102
[71] -0.139818719 -1.891135351 -2.131477696 0.825593104 0.303848440
[76] -0.593174334 -0.192954039 1.279718511 0.618252600 -0.519520224
[81] -2.727924893 -0.023162340 -2.233303638 2.077439245 0.598040909
[86] -0.937305905 0.648613976 -0.147604962 -0.001565387 0.946162595
[91] -0.089111809 -0.040589582 -1.599463870 -0.223422338 -0.246624868
[96] -1.103711548 -1.846408658 -0.185648854 0.170592953 -2.119948650
> colMin(tmp)
[1] 1.224332013 -1.048779693 0.685835383 -0.027251408 -1.228547516
[6] -0.300622584 0.272407136 -0.755581494 0.077293788 -0.434769064
[11] -1.539016737 1.460704352 -0.973724781 0.965343333 -1.905663846
[16] -0.836053177 -0.148991142 -0.869913438 1.402276665 -1.547380001
[21] -0.631206211 1.592475825 0.029519451 1.002483237 -2.839438775
[26] 1.097318980 -0.137893350 2.935884988 -0.012061189 0.331061045
[31] 0.542748709 0.312860045 2.354616384 0.447634843 -1.909348008
[36] 0.250222220 0.475458107 0.162789723 -1.462369819 -1.969822606
[41] -0.081645611 -0.626761054 1.510348966 0.488548010 0.217891024
[46] 0.883408682 0.205482100 -1.833090844 -0.360412601 -1.322424259
[51] -0.179567832 0.727090127 1.265254006 -2.196918183 -0.020940069
[56] 0.501663551 -1.217610625 0.360446305 0.230213164 0.603788662
[61] 1.114155970 -0.003230589 -0.487628051 -0.890199831 1.931259665
[66] -0.387791754 0.062254225 0.873104942 -0.249700117 0.332699102
[71] -0.139818719 -1.891135351 -2.131477696 0.825593104 0.303848440
[76] -0.593174334 -0.192954039 1.279718511 0.618252600 -0.519520224
[81] -2.727924893 -0.023162340 -2.233303638 2.077439245 0.598040909
[86] -0.937305905 0.648613976 -0.147604962 -0.001565387 0.946162595
[91] -0.089111809 -0.040589582 -1.599463870 -0.223422338 -0.246624868
[96] -1.103711548 -1.846408658 -0.185648854 0.170592953 -2.119948650
> colMedians(tmp)
[1] 1.224332013 -1.048779693 0.685835383 -0.027251408 -1.228547516
[6] -0.300622584 0.272407136 -0.755581494 0.077293788 -0.434769064
[11] -1.539016737 1.460704352 -0.973724781 0.965343333 -1.905663846
[16] -0.836053177 -0.148991142 -0.869913438 1.402276665 -1.547380001
[21] -0.631206211 1.592475825 0.029519451 1.002483237 -2.839438775
[26] 1.097318980 -0.137893350 2.935884988 -0.012061189 0.331061045
[31] 0.542748709 0.312860045 2.354616384 0.447634843 -1.909348008
[36] 0.250222220 0.475458107 0.162789723 -1.462369819 -1.969822606
[41] -0.081645611 -0.626761054 1.510348966 0.488548010 0.217891024
[46] 0.883408682 0.205482100 -1.833090844 -0.360412601 -1.322424259
[51] -0.179567832 0.727090127 1.265254006 -2.196918183 -0.020940069
[56] 0.501663551 -1.217610625 0.360446305 0.230213164 0.603788662
[61] 1.114155970 -0.003230589 -0.487628051 -0.890199831 1.931259665
[66] -0.387791754 0.062254225 0.873104942 -0.249700117 0.332699102
[71] -0.139818719 -1.891135351 -2.131477696 0.825593104 0.303848440
[76] -0.593174334 -0.192954039 1.279718511 0.618252600 -0.519520224
[81] -2.727924893 -0.023162340 -2.233303638 2.077439245 0.598040909
[86] -0.937305905 0.648613976 -0.147604962 -0.001565387 0.946162595
[91] -0.089111809 -0.040589582 -1.599463870 -0.223422338 -0.246624868
[96] -1.103711548 -1.846408658 -0.185648854 0.170592953 -2.119948650
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] 1.224332 -1.04878 0.6858354 -0.02725141 -1.228548 -0.3006226 0.2724071
[2,] 1.224332 -1.04878 0.6858354 -0.02725141 -1.228548 -0.3006226 0.2724071
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] -0.7555815 0.07729379 -0.4347691 -1.539017 1.460704 -0.9737248 0.9653433
[2,] -0.7555815 0.07729379 -0.4347691 -1.539017 1.460704 -0.9737248 0.9653433
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] -1.905664 -0.8360532 -0.1489911 -0.8699134 1.402277 -1.54738 -0.6312062
[2,] -1.905664 -0.8360532 -0.1489911 -0.8699134 1.402277 -1.54738 -0.6312062
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] 1.592476 0.02951945 1.002483 -2.839439 1.097319 -0.1378934 2.935885
[2,] 1.592476 0.02951945 1.002483 -2.839439 1.097319 -0.1378934 2.935885
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] -0.01206119 0.331061 0.5427487 0.31286 2.354616 0.4476348 -1.909348
[2,] -0.01206119 0.331061 0.5427487 0.31286 2.354616 0.4476348 -1.909348
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] 0.2502222 0.4754581 0.1627897 -1.46237 -1.969823 -0.08164561 -0.6267611
[2,] 0.2502222 0.4754581 0.1627897 -1.46237 -1.969823 -0.08164561 -0.6267611
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] 1.510349 0.488548 0.217891 0.8834087 0.2054821 -1.833091 -0.3604126
[2,] 1.510349 0.488548 0.217891 0.8834087 0.2054821 -1.833091 -0.3604126
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] -1.322424 -0.1795678 0.7270901 1.265254 -2.196918 -0.02094007 0.5016636
[2,] -1.322424 -0.1795678 0.7270901 1.265254 -2.196918 -0.02094007 0.5016636
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] -1.217611 0.3604463 0.2302132 0.6037887 1.114156 -0.003230589 -0.4876281
[2,] -1.217611 0.3604463 0.2302132 0.6037887 1.114156 -0.003230589 -0.4876281
[,64] [,65] [,66] [,67] [,68] [,69] [,70]
[1,] -0.8901998 1.93126 -0.3877918 0.06225422 0.8731049 -0.2497001 0.3326991
[2,] -0.8901998 1.93126 -0.3877918 0.06225422 0.8731049 -0.2497001 0.3326991
[,71] [,72] [,73] [,74] [,75] [,76] [,77]
[1,] -0.1398187 -1.891135 -2.131478 0.8255931 0.3038484 -0.5931743 -0.192954
[2,] -0.1398187 -1.891135 -2.131478 0.8255931 0.3038484 -0.5931743 -0.192954
[,78] [,79] [,80] [,81] [,82] [,83] [,84]
[1,] 1.279719 0.6182526 -0.5195202 -2.727925 -0.02316234 -2.233304 2.077439
[2,] 1.279719 0.6182526 -0.5195202 -2.727925 -0.02316234 -2.233304 2.077439
[,85] [,86] [,87] [,88] [,89] [,90] [,91]
[1,] 0.5980409 -0.9373059 0.648614 -0.147605 -0.001565387 0.9461626 -0.08911181
[2,] 0.5980409 -0.9373059 0.648614 -0.147605 -0.001565387 0.9461626 -0.08911181
[,92] [,93] [,94] [,95] [,96] [,97] [,98]
[1,] -0.04058958 -1.599464 -0.2234223 -0.2466249 -1.103712 -1.846409 -0.1856489
[2,] -0.04058958 -1.599464 -0.2234223 -0.2466249 -1.103712 -1.846409 -0.1856489
[,99] [,100]
[1,] 0.170593 -2.119949
[2,] 0.170593 -2.119949
>
>
> Max(tmp2)
[1] 3.108192
> Min(tmp2)
[1] -2.568265
> mean(tmp2)
[1] 0.2159037
> Sum(tmp2)
[1] 21.59037
> Var(tmp2)
[1] 1.073317
>
> rowMeans(tmp2)
[1] -1.07849841 0.97252139 1.67752539 0.13247123 1.31938694 0.76015945
[7] -0.02867098 1.23300459 0.17610521 -2.05695188 0.26435483 0.22522615
[13] 0.94542300 0.34397950 0.28099685 0.53094382 1.37283984 0.38120472
[19] 1.25281881 0.97920764 0.20402143 0.46161060 1.13380071 0.46694330
[25] 0.41343904 -0.16880158 -0.25954277 2.02392031 0.58419815 0.78519898
[31] 0.18167413 -0.06207318 1.34726993 -0.21400540 1.50945323 -0.38914814
[37] -0.70060268 -0.10276230 2.10425650 0.64716031 -0.02446814 0.73724470
[43] -0.53402219 -0.35922913 0.85515613 0.28478548 0.45257598 0.27341748
[49] 1.29918755 0.82278045 -0.39841412 1.22360159 0.43546762 -0.02605712
[55] 0.58187778 1.50630760 0.37477460 0.28762549 1.78885434 0.54516347
[61] -1.76526682 0.71632178 1.06611300 -0.34674957 -0.99617567 -1.35437205
[67] 0.10354350 0.43813934 1.79544749 0.23825270 1.47316922 0.46191701
[73] 0.96431760 3.10819234 -0.29629704 0.43227533 -0.35531771 -0.21298122
[79] -2.56826505 -1.03526085 -2.44765038 -1.00553726 -0.64193287 1.40410303
[85] -1.03630801 -0.54859192 -0.79124761 0.63382476 1.17806901 1.65002719
[91] -0.74449321 -0.90074721 0.99420818 -0.27688011 -1.06266088 -0.82076217
[97] -1.98080468 -1.51083111 -1.95500943 -0.19009464
> rowSums(tmp2)
[1] -1.07849841 0.97252139 1.67752539 0.13247123 1.31938694 0.76015945
[7] -0.02867098 1.23300459 0.17610521 -2.05695188 0.26435483 0.22522615
[13] 0.94542300 0.34397950 0.28099685 0.53094382 1.37283984 0.38120472
[19] 1.25281881 0.97920764 0.20402143 0.46161060 1.13380071 0.46694330
[25] 0.41343904 -0.16880158 -0.25954277 2.02392031 0.58419815 0.78519898
[31] 0.18167413 -0.06207318 1.34726993 -0.21400540 1.50945323 -0.38914814
[37] -0.70060268 -0.10276230 2.10425650 0.64716031 -0.02446814 0.73724470
[43] -0.53402219 -0.35922913 0.85515613 0.28478548 0.45257598 0.27341748
[49] 1.29918755 0.82278045 -0.39841412 1.22360159 0.43546762 -0.02605712
[55] 0.58187778 1.50630760 0.37477460 0.28762549 1.78885434 0.54516347
[61] -1.76526682 0.71632178 1.06611300 -0.34674957 -0.99617567 -1.35437205
[67] 0.10354350 0.43813934 1.79544749 0.23825270 1.47316922 0.46191701
[73] 0.96431760 3.10819234 -0.29629704 0.43227533 -0.35531771 -0.21298122
[79] -2.56826505 -1.03526085 -2.44765038 -1.00553726 -0.64193287 1.40410303
[85] -1.03630801 -0.54859192 -0.79124761 0.63382476 1.17806901 1.65002719
[91] -0.74449321 -0.90074721 0.99420818 -0.27688011 -1.06266088 -0.82076217
[97] -1.98080468 -1.51083111 -1.95500943 -0.19009464
> rowVars(tmp2)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> rowSd(tmp2)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> rowMax(tmp2)
[1] -1.07849841 0.97252139 1.67752539 0.13247123 1.31938694 0.76015945
[7] -0.02867098 1.23300459 0.17610521 -2.05695188 0.26435483 0.22522615
[13] 0.94542300 0.34397950 0.28099685 0.53094382 1.37283984 0.38120472
[19] 1.25281881 0.97920764 0.20402143 0.46161060 1.13380071 0.46694330
[25] 0.41343904 -0.16880158 -0.25954277 2.02392031 0.58419815 0.78519898
[31] 0.18167413 -0.06207318 1.34726993 -0.21400540 1.50945323 -0.38914814
[37] -0.70060268 -0.10276230 2.10425650 0.64716031 -0.02446814 0.73724470
[43] -0.53402219 -0.35922913 0.85515613 0.28478548 0.45257598 0.27341748
[49] 1.29918755 0.82278045 -0.39841412 1.22360159 0.43546762 -0.02605712
[55] 0.58187778 1.50630760 0.37477460 0.28762549 1.78885434 0.54516347
[61] -1.76526682 0.71632178 1.06611300 -0.34674957 -0.99617567 -1.35437205
[67] 0.10354350 0.43813934 1.79544749 0.23825270 1.47316922 0.46191701
[73] 0.96431760 3.10819234 -0.29629704 0.43227533 -0.35531771 -0.21298122
[79] -2.56826505 -1.03526085 -2.44765038 -1.00553726 -0.64193287 1.40410303
[85] -1.03630801 -0.54859192 -0.79124761 0.63382476 1.17806901 1.65002719
[91] -0.74449321 -0.90074721 0.99420818 -0.27688011 -1.06266088 -0.82076217
[97] -1.98080468 -1.51083111 -1.95500943 -0.19009464
> rowMin(tmp2)
[1] -1.07849841 0.97252139 1.67752539 0.13247123 1.31938694 0.76015945
[7] -0.02867098 1.23300459 0.17610521 -2.05695188 0.26435483 0.22522615
[13] 0.94542300 0.34397950 0.28099685 0.53094382 1.37283984 0.38120472
[19] 1.25281881 0.97920764 0.20402143 0.46161060 1.13380071 0.46694330
[25] 0.41343904 -0.16880158 -0.25954277 2.02392031 0.58419815 0.78519898
[31] 0.18167413 -0.06207318 1.34726993 -0.21400540 1.50945323 -0.38914814
[37] -0.70060268 -0.10276230 2.10425650 0.64716031 -0.02446814 0.73724470
[43] -0.53402219 -0.35922913 0.85515613 0.28478548 0.45257598 0.27341748
[49] 1.29918755 0.82278045 -0.39841412 1.22360159 0.43546762 -0.02605712
[55] 0.58187778 1.50630760 0.37477460 0.28762549 1.78885434 0.54516347
[61] -1.76526682 0.71632178 1.06611300 -0.34674957 -0.99617567 -1.35437205
[67] 0.10354350 0.43813934 1.79544749 0.23825270 1.47316922 0.46191701
[73] 0.96431760 3.10819234 -0.29629704 0.43227533 -0.35531771 -0.21298122
[79] -2.56826505 -1.03526085 -2.44765038 -1.00553726 -0.64193287 1.40410303
[85] -1.03630801 -0.54859192 -0.79124761 0.63382476 1.17806901 1.65002719
[91] -0.74449321 -0.90074721 0.99420818 -0.27688011 -1.06266088 -0.82076217
[97] -1.98080468 -1.51083111 -1.95500943 -0.19009464
>
> colMeans(tmp2)
[1] 0.2159037
> colSums(tmp2)
[1] 21.59037
> colVars(tmp2)
[1] 1.073317
> colSd(tmp2)
[1] 1.03601
> colMax(tmp2)
[1] 3.108192
> colMin(tmp2)
[1] -2.568265
> colMedians(tmp2)
[1] 0.2862055
> colRanges(tmp2)
[,1]
[1,] -2.568265
[2,] 3.108192
>
> dataset1 <- matrix(dataset1,1,100)
>
> agree.checks(tmp,dataset1)
>
> dataset2 <- matrix(dataset2,100,1)
> agree.checks(tmp2,dataset2)
>
>
> tmp <- createBufferedMatrix(10,10)
>
> tmp[1:10,1:10] <- rnorm(100)
> colApply(tmp,sum)
[1] -2.3272018 -1.5928967 1.9953224 2.7656755 1.6860252 -4.0891587
[7] -0.6035578 -4.4735060 -0.2218258 -3.8645059
> colApply(tmp,quantile)[,1]
[,1]
[1,] -2.02295530
[2,] -0.73921633
[3,] -0.07362537
[4,] 0.52669360
[5,] 1.08963799
>
> rowApply(tmp,sum)
[1] 2.2330258 -4.7657496 2.8282665 -0.6874828 -3.1576675 0.1460196
[7] 0.5232884 -2.3390601 -1.3338494 -4.1724207
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 2 7 6 8 5 10 9 8 2 1
[2,] 1 9 2 3 3 9 4 3 9 8
[3,] 10 10 10 7 4 6 5 2 1 4
[4,] 6 4 7 5 6 4 8 9 10 7
[5,] 7 3 9 4 10 5 2 10 4 5
[6,] 3 1 1 9 2 7 7 4 3 9
[7,] 9 8 4 10 1 3 1 5 5 6
[8,] 4 6 3 2 9 2 3 7 8 2
[9,] 8 2 5 6 8 8 10 6 7 3
[10,] 5 5 8 1 7 1 6 1 6 10
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] 3.64093204 2.95799289 3.71593635 0.37647082 2.33868599 2.18015145
[7] -0.22064103 1.84903602 0.79534381 -3.58692665 0.14821554 0.41661909
[13] 2.68051786 -1.20195325 3.79386139 0.39521712 -1.93028998 1.85330797
[19] 0.07810732 -0.43447826
> colApply(tmp,quantile)[,1]
[,1]
[1,] 0.08336414
[2,] 0.63120130
[3,] 0.91521130
[4,] 0.95807415
[5,] 1.05308115
>
> rowApply(tmp,sum)
[1] -3.623726 5.301775 6.719838 10.167303 1.280917
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 11 19 14 12 17
[2,] 8 20 15 1 20
[3,] 17 3 16 19 12
[4,] 18 1 2 13 13
[5,] 13 15 18 8 7
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 0.08336414 -0.5812726 0.7948212 0.9779048 0.34872188 1.3967783
[2,] 1.05308115 2.2016563 -0.4724421 -0.6241205 0.51961360 0.2749250
[3,] 0.95807415 1.1362956 1.1420523 -1.1057433 1.85904941 0.0836558
[4,] 0.63120130 -1.0785945 1.8538109 0.6551134 0.05562539 1.1717173
[5,] 0.91521130 1.2799081 0.3976941 0.4733163 -0.44432430 -0.7469250
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] -0.8281760 -0.6022411 0.44808103 -2.7154149 1.257396 -0.4690542
[2,] -0.2078263 0.6475900 -0.61207127 0.3249957 0.718792 0.2181061
[3,] -0.8644405 2.1341675 0.02298839 -0.4382113 -2.208635 0.2767304
[4,] 3.0742533 -0.5268299 0.09178320 -0.1613636 1.471763 1.6303947
[5,] -1.3944514 0.1963495 0.84456245 -0.5969325 -1.091101 -1.2395579
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] 0.34181211 -0.4523202 0.7480438 -1.1600824 -1.7956441 -0.785230190
[2,] 0.05533248 -0.4589065 0.1014291 0.1781606 0.2310431 -0.004391056
[3,] 1.52298341 0.3200116 2.4043445 0.6202372 -0.7489970 0.003411567
[4,] -0.14016979 -0.1788917 1.0241628 -0.3731353 0.1117348 1.721111827
[5,] 0.90055964 -0.4318465 -0.4841188 1.1300371 0.2715732 0.918405818
[,19] [,20]
[1,] 0.6401070 -1.2713199
[2,] 0.4517785 0.7050286
[3,] 0.4606806 -0.8588174
[4,] -1.0334860 0.1671014
[5,] -0.4409728 0.8235291
>
>
> is.BufferedMatrix(tmp)
[1] TRUE
>
> as.BufferedMatrix(as.matrix(tmp))
BufferedMatrix object
Matrix size: 5 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 800 bytes.
>
>
>
> subBufferedMatrix(tmp,1:5,1:5)
BufferedMatrix object
Matrix size: 5 5
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 654 bytes.
Disk usage : 200 bytes.
> subBufferedMatrix(tmp,,5:8)
BufferedMatrix object
Matrix size: 5 4
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 566 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 -1.134953 -1.185749 -1.169179 1.031418 0.3806285 0.4058019 -0.1181772
col8 col9 col10 col11 col12 col13 col14
row1 0.4277884 1.524897 1.101451 0.4913279 0.2644853 -0.7270644 -1.137236
col15 col16 col17 col18 col19 col20
row1 0.06248261 0.2832514 0.9664387 2.132792 1.482931 -1.817232
> tmp[,"col10"]
col10
row1 1.10145128
row2 -0.27708927
row3 -0.17598236
row4 -0.09347051
row5 0.82225127
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7
row1 -1.1349534 -1.185749 -1.169179 1.031418 0.3806285 0.4058019 -0.1181772
row5 -0.2989438 1.166394 1.254955 -1.662940 -0.1830673 -0.3178712 0.7740699
col8 col9 col10 col11 col12 col13 col14
row1 0.4277884 1.5248969 1.1014513 0.4913279 0.2644853 -0.7270644 -1.1372362
row5 1.9443520 0.0653305 0.8222513 0.5134618 1.5981045 -2.1119173 -0.6770254
col15 col16 col17 col18 col19 col20
row1 0.06248261 0.2832514 0.9664387 2.1327925 1.482931 -1.817232
row5 0.24107186 0.2040926 0.5073436 -0.8748657 0.493653 1.384498
> tmp[,c("col6","col20")]
col6 col20
row1 0.4058019 -1.8172321
row2 1.1248692 -0.1310904
row3 -0.6266119 0.8102029
row4 -0.2862664 -0.7410656
row5 -0.3178712 1.3844984
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 0.4058019 -1.817232
row5 -0.3178712 1.384498
>
>
>
>
> 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 53.36501 50.86423 49.67843 49.8587 52.32812 105.0908 50.48139 50.03965
col9 col10 col11 col12 col13 col14 col15 col16
row1 51.26914 50.65649 50.68166 48.86529 50.69737 50.51873 50.69444 49.68764
col17 col18 col19 col20
row1 49.67984 50.35784 49.39567 106.3961
> tmp[,"col10"]
col10
row1 50.65649
row2 29.93770
row3 31.17399
row4 28.77244
row5 51.41938
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 53.36501 50.86423 49.67843 49.85870 52.32812 105.0908 50.48139 50.03965
row5 50.71075 50.53163 48.97660 50.35023 50.87374 104.0792 50.06809 49.68851
col9 col10 col11 col12 col13 col14 col15 col16
row1 51.26914 50.65649 50.68166 48.86529 50.69737 50.51873 50.69444 49.68764
row5 50.54592 51.41938 50.29653 50.10047 50.34201 51.00025 50.65270 50.28944
col17 col18 col19 col20
row1 49.67984 50.35784 49.39567 106.3961
row5 50.87221 48.75223 48.95306 105.6394
> tmp[,c("col6","col20")]
col6 col20
row1 105.09084 106.39609
row2 75.68172 76.16962
row3 76.00518 74.81824
row4 74.33088 75.99112
row5 104.07921 105.63940
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 105.0908 106.3961
row5 104.0792 105.6394
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 105.0908 106.3961
row5 104.0792 105.6394
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] 1.7562959
[2,] -1.0341561
[3,] 1.3400895
[4,] -0.7207185
[5,] -0.6598835
> tmp[,c("col17","col7")]
col17 col7
[1,] 1.1244925 -0.98443383
[2,] -0.2373432 0.18147772
[3,] 1.1344713 0.04695115
[4,] 0.1178302 -0.36367901
[5,] -1.1450929 -0.95904887
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] -0.7635864 -0.2673039
[2,] -0.5988553 0.3498553
[3,] -0.5208310 0.1808832
[4,] 1.7990321 -2.8033295
[5,] -0.4052516 1.8501486
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] -0.7635864
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] -0.7635864
[2,] -0.5988553
>
>
>
> 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 -2.242181 0.4094070 0.5594772 -0.3309658 0.37196626 2.2659846 -0.3222741
row1 -0.242398 0.3156548 0.5006338 -1.7915415 0.08316888 -0.7530142 -0.3668215
[,8] [,9] [,10] [,11] [,12] [,13]
row3 0.31327207 0.07045103 1.455150 0.4385885 1.117776896 0.1845462
row1 0.08158344 -0.59235823 -1.565212 -1.5466757 -0.001965176 0.1217539
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
row3 2.223147 -0.937494 -0.3113453 0.8656732 0.5378125 0.06913177 0.1373294
row1 -2.181465 1.693282 -0.3371116 1.7828253 0.7136729 -1.00872135 -1.2904251
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 0.4246416 0.3699834 -0.7775909 0.9133625 -2.15347 -0.6492323 -0.1796635
[,8] [,9] [,10]
row2 1.244099 1.8327 -0.5601595
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 -0.2251437 -0.6459669 -1.851823 0.3388993 -1.058583 -1.286579 -0.1204601
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 -0.099261 0.4992419 0.1054536 0.8453506 -0.8038399 -1.124231 1.469286
[,15] [,16] [,17] [,18] [,19] [,20]
row5 -2.279349 0.304852 0.719379 -0.4041101 -0.04316917 0.6838007
>
>
> 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: 0x65148f593000>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2274e6622c5307"
[2] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2274e62a23b8ee"
[3] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2274e62efebee7"
[4] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2274e61dec0ead"
[5] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2274e6daf57a3"
[6] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2274e63ebe3cff"
[7] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2274e668d32f57"
[8] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2274e66f5132eb"
[9] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2274e66a657b25"
[10] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2274e670fc6dad"
[11] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2274e6210fa015"
[12] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2274e625818ad3"
[13] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2274e61a9ab5be"
[14] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2274e6785c0054"
[15] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2274e669f1a89e"
>
>
> ### 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: 0x65148fbe5250>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x65148fbe5250>
Warning message:
In dir.create(new.directory) :
'/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x65148fbe5250>
> rowMedians(tmp)
[1] -0.253851704 0.032813699 -0.265713192 0.084884151 -0.373657513
[6] 0.249760728 -0.009519743 0.197733926 0.155592539 0.626147148
[11] -0.137227628 0.337387929 -0.546346698 -0.605140770 0.313956520
[16] -0.065094101 -0.566030858 -0.273558858 -0.388698540 0.478653376
[21] 0.415425294 -0.250284292 0.155031171 0.692893183 0.183105330
[26] 1.011858875 0.125476258 -0.655136935 0.014334444 -0.321018714
[31] 0.313026488 0.081226059 0.136903045 -0.113746024 0.018968701
[36] 0.178090902 0.023369809 -0.045851342 0.134110767 -0.414446260
[41] -0.284356997 -0.256881351 -0.148538886 -0.400228602 0.044880978
[46] -0.345913640 0.188773141 0.206355207 0.041065150 -0.721073597
[51] 0.164216728 0.275184264 -0.212207879 -0.105997889 -0.034250761
[56] -0.447272033 -0.089656693 0.043118443 -0.163655540 0.195739859
[61] 0.100727697 -0.501171625 -0.202832868 -0.057937816 0.152547944
[66] 0.048045646 0.015440731 0.030810532 0.137408412 0.056559109
[71] 0.243259135 -0.506076082 0.202149744 -0.518762734 -0.163567193
[76] 0.609835193 0.258466565 0.564843224 0.092600944 0.229445433
[81] 0.029608314 0.478313440 0.015527712 0.092165427 -0.014709933
[86] 0.034949057 -0.150775705 -0.085023911 -0.175799405 0.542332064
[91] -0.183605959 0.063856702 0.293908138 0.457158970 -0.056445019
[96] -0.027894522 0.159418344 -0.199609974 0.354290066 0.069369489
[101] 0.243524134 0.532517290 0.285937933 -0.258726353 0.359451685
[106] 0.329943115 0.288179451 -0.002865006 0.347906518 0.215995858
[111] -0.416840028 -0.576426685 -0.202852841 0.041602459 -0.197393865
[116] -0.174732986 0.171996855 -0.159541679 0.458143775 0.276517001
[121] 0.244144698 -0.341581751 -0.542096633 -0.160146785 0.204605250
[126] 0.723899593 0.028464729 -0.257710230 0.382864937 -0.446933897
[131] 0.281669779 -0.787938260 -0.758902673 0.542567996 -0.175419542
[136] 0.021538492 0.128661567 -0.159070718 0.105730688 -0.438466817
[141] 0.086423354 0.272153204 0.050445267 0.157647242 -0.501576872
[146] -0.900042989 -0.266473452 -0.341020510 0.092437152 0.032553626
[151] 0.017272452 0.126933503 -0.032411501 0.149633358 0.288539297
[156] -0.069550858 -0.205131010 -0.092114239 0.651702290 0.103566761
[161] 0.122434561 0.108485931 0.305585681 -0.088365321 0.124225133
[166] 0.145822068 -0.126865733 -0.530948669 0.055560764 0.544785607
[171] 0.431899755 0.124076031 0.458998150 0.492776010 -0.032959947
[176] -0.556529012 0.151389870 0.089612196 -0.283879370 0.314790281
[181] 0.359210131 -0.072394424 -0.380459250 0.062359668 0.268346119
[186] 0.317350814 -0.411933772 -0.704671542 -0.279548095 0.115879945
[191] 0.673280490 -0.105015573 0.035691642 -0.679160384 0.300027192
[196] 0.073946191 0.562860138 0.326346637 -0.249111082 0.219651366
[201] 0.002578775 0.079413540 -0.304995236 -0.142643044 0.080812361
[206] 0.009085615 -0.459319488 -0.472744107 0.138867907 -0.422711967
[211] 0.278342171 0.406624462 0.189159343 -0.095150437 0.089183066
[216] 0.311469404 0.718572995 0.009402251 0.494008542 -0.185733478
[221] -0.692615178 -0.155738073 -0.150940711 0.140302771 -0.033068345
[226] 0.458826626 0.286659212 0.507860320 -0.587278836 0.351336941
>
> proc.time()
user system elapsed
1.278 0.674 1.940
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: 0x589079b25370>
> .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: 0x589079b25370>
> .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: 0x589079b25370>
> .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: 0x589079b25370>
> 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: 0x589079b0d1c0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x589079b0d1c0>
> .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: 0x589079b0d1c0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x589079b0d1c0>
> .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: 0x589079b0d1c0>
> 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: 0x589079df0120>
> .Call("R_bm_AddColumn",P)
<pointer: 0x589079df0120>
> .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: 0x589079df0120>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x589079df0120>
> .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: 0x589079df0120>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x589079df0120>
> .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: 0x589079df0120>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x589079df0120>
> .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: 0x589079df0120>
> 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: 0x589078b40390>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x589078b40390>
> .Call("R_bm_AddColumn",P)
<pointer: 0x589078b40390>
> .Call("R_bm_AddColumn",P)
<pointer: 0x589078b40390>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile2275f63b159b43" "BufferedMatrixFile2275f6afa9570"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile2275f63b159b43" "BufferedMatrixFile2275f6afa9570"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x589078a373d0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x589078a373d0>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x589078a373d0>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x589078a373d0>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x589078a373d0>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x589078a373d0>
> .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: 0x58907a56cfa0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x58907a56cfa0>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x58907a56cfa0>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x58907a56cfa0>
> 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: 0x589078d44ff0>
> .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: 0x589078d44ff0>
> rm(P)
>
> proc.time()
user system elapsed
0.246 0.051 0.285
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
0.240 0.053 0.282