Ben Bolstad
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/BufferedMatrix |
| Branch: master |
| Last Commit: eca2e36 |
| Last Changed Date: 2018-10-30 11:54:27 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:23:42 -0400 (Tue, 09 Apr 2019).
| Package 190/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BufferedMatrix 1.47.0 Ben Bolstad
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK |
| Package: BufferedMatrix |
| Version: 1.47.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BufferedMatrix_1.47.0.tar.gz |
| StartedAt: 2019-04-08 23:36:41 -0400 (Mon, 08 Apr 2019) |
| EndedAt: 2019-04-08 23:37:25 -0400 (Mon, 08 Apr 2019) |
| EllapsedTime: 43.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BufferedMatrix.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BufferedMatrix_1.47.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/BufferedMatrix.Rcheck’ * using R Under development (unstable) (2018-11-27 r75683) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘BufferedMatrix/DESCRIPTION’ ... OK * this is package ‘BufferedMatrix’ version ‘1.47.0’ * 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 * 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 R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... NOTE prepare_Rd: createBufferedMatrix.Rd:26: Dropping empty section \keyword prepare_Rd: createBufferedMatrix.Rd:17-18: Dropping empty section \details prepare_Rd: createBufferedMatrix.Rd:15-16: Dropping empty section \value prepare_Rd: createBufferedMatrix.Rd:19-20: Dropping empty section \references prepare_Rd: createBufferedMatrix.Rd:21-22: Dropping empty section \seealso prepare_Rd: createBufferedMatrix.Rd:23-24: Dropping empty section \examples * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... NONE * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘Rcodetesting.R’ Running ‘c_code_level_tests.R’ Running ‘objectTesting.R’ Running ‘rawCalltesting.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/Users/biocbuild/bbs-3.9-bioc/meat/BufferedMatrix.Rcheck/00check.log’ for details.
BufferedMatrix.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BufferedMatrix
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘BufferedMatrix’ ...
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c RBufferedMatrix.c -o RBufferedMatrix.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c doubleBufferedMatrix.c -o doubleBufferedMatrix.o
doubleBufferedMatrix.c:1580:7: warning: logical not is only applied to the left hand side of this bitwise operator [-Wlogical-not-parentheses]
if (!(Matrix->readonly) & setting){
^ ˜
doubleBufferedMatrix.c:1580:7: note: add parentheses after the '!' to evaluate the bitwise operator first
if (!(Matrix->readonly) & setting){
^
( )
doubleBufferedMatrix.c:1580:7: note: add parentheses around left hand side expression to silence this warning
if (!(Matrix->readonly) & setting){
^
( )
doubleBufferedMatrix.c:3327:12: warning: unused function 'sort_double' [-Wunused-function]
static int sort_double(const double *a1,const double *a2){
^
2 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c doubleBufferedMatrix_C_tests.c -o doubleBufferedMatrix_C_tests.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c init_package.c -o init_package.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o BufferedMatrix.so RBufferedMatrix.o doubleBufferedMatrix.o doubleBufferedMatrix_C_tests.o init_package.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/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
* DONE (BufferedMatrix)
BufferedMatrix.Rcheck/tests/c_code_level_tests.Rout
R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
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
0.425 0.111 0.506
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths());
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
>
>
> ### this is used to control how many repetitions in something below
> ### higher values result in more checks.
> nreps <-100 ##20000
>
>
> ## test creation and some simple assignments and subsetting operations
>
> ## first on single elements
> tmp <- createBufferedMatrix(1000,10)
>
> tmp[10,5]
[1] 0
> tmp[10,5] <- 10
> tmp[10,5]
[1] 10
> tmp[10,5] <- 12.445
> tmp[10,5]
[1] 12.445
>
>
>
> ## now testing accessing multiple elements
> tmp2 <- createBufferedMatrix(10,20)
>
>
> tmp2[3,1] <- 51.34
> tmp2[9,2] <- 9.87654
> tmp2[,1:2]
[,1] [,2]
[1,] 0.00 0.00000
[2,] 0.00 0.00000
[3,] 51.34 0.00000
[4,] 0.00 0.00000
[5,] 0.00 0.00000
[6,] 0.00 0.00000
[7,] 0.00 0.00000
[8,] 0.00 0.00000
[9,] 0.00 9.87654
[10,] 0.00 0.00000
> tmp2[,-(3:20)]
[,1] [,2]
[1,] 0.00 0.00000
[2,] 0.00 0.00000
[3,] 51.34 0.00000
[4,] 0.00 0.00000
[5,] 0.00 0.00000
[6,] 0.00 0.00000
[7,] 0.00 0.00000
[8,] 0.00 0.00000
[9,] 0.00 9.87654
[10,] 0.00 0.00000
> tmp2[3,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 51.34 0 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
[1,] 0 0 0 0 0 0 0
> tmp2[-3,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[2,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[3,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[4,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[5,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[6,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[7,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[8,] 0 9.87654 0 0 0 0 0 0 0 0 0 0 0
[9,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
[1,] 0 0 0 0 0 0 0
[2,] 0 0 0 0 0 0 0
[3,] 0 0 0 0 0 0 0
[4,] 0 0 0 0 0 0 0
[5,] 0 0 0 0 0 0 0
[6,] 0 0 0 0 0 0 0
[7,] 0 0 0 0 0 0 0
[8,] 0 0 0 0 0 0 0
[9,] 0 0 0 0 0 0 0
> tmp2[2,1:3]
[,1] [,2] [,3]
[1,] 0 0 0
> tmp2[3:9,1:3]
[,1] [,2] [,3]
[1,] 51.34 0.00000 0
[2,] 0.00 0.00000 0
[3,] 0.00 0.00000 0
[4,] 0.00 0.00000 0
[5,] 0.00 0.00000 0
[6,] 0.00 0.00000 0
[7,] 0.00 9.87654 0
> tmp2[-4,-4]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[2,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[3,] 51.34 0.00000 0 0 0 0 0 0 0 0 0 0 0
[4,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[5,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[6,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[7,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[8,] 0.00 9.87654 0 0 0 0 0 0 0 0 0 0 0
[9,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19]
[1,] 0 0 0 0 0 0
[2,] 0 0 0 0 0 0
[3,] 0 0 0 0 0 0
[4,] 0 0 0 0 0 0
[5,] 0 0 0 0 0 0
[6,] 0 0 0 0 0 0
[7,] 0 0 0 0 0 0
[8,] 0 0 0 0 0 0
[9,] 0 0 0 0 0 0
>
> ## now testing accessing/assigning multiple elements
> tmp3 <- createBufferedMatrix(10,10)
>
> for (i in 1:10){
+ for (j in 1:10){
+ tmp3[i,j] <- (j-1)*10 + i
+ }
+ }
>
> tmp3[2:4,2:4]
[,1] [,2] [,3]
[1,] 12 22 32
[2,] 13 23 33
[3,] 14 24 34
> tmp3[c(-10),c(2:4,2:4,10,1,2,1:10,10:1)]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 11 21 31 11 21 31 91 1 11 1 11 21 31
[2,] 12 22 32 12 22 32 92 2 12 2 12 22 32
[3,] 13 23 33 13 23 33 93 3 13 3 13 23 33
[4,] 14 24 34 14 24 34 94 4 14 4 14 24 34
[5,] 15 25 35 15 25 35 95 5 15 5 15 25 35
[6,] 16 26 36 16 26 36 96 6 16 6 16 26 36
[7,] 17 27 37 17 27 37 97 7 17 7 17 27 37
[8,] 18 28 38 18 28 38 98 8 18 8 18 28 38
[9,] 19 29 39 19 29 39 99 9 19 9 19 29 39
[,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25]
[1,] 41 51 61 71 81 91 91 81 71 61 51 41
[2,] 42 52 62 72 82 92 92 82 72 62 52 42
[3,] 43 53 63 73 83 93 93 83 73 63 53 43
[4,] 44 54 64 74 84 94 94 84 74 64 54 44
[5,] 45 55 65 75 85 95 95 85 75 65 55 45
[6,] 46 56 66 76 86 96 96 86 76 66 56 46
[7,] 47 57 67 77 87 97 97 87 77 67 57 47
[8,] 48 58 68 78 88 98 98 88 78 68 58 48
[9,] 49 59 69 79 89 99 99 89 79 69 59 49
[,26] [,27] [,28] [,29]
[1,] 31 21 11 1
[2,] 32 22 12 2
[3,] 33 23 13 3
[4,] 34 24 14 4
[5,] 35 25 15 5
[6,] 36 26 16 6
[7,] 37 27 17 7
[8,] 38 28 18 8
[9,] 39 29 19 9
> tmp3[-c(1:5),-c(6:10)]
[,1] [,2] [,3] [,4] [,5]
[1,] 6 16 26 36 46
[2,] 7 17 27 37 47
[3,] 8 18 28 38 48
[4,] 9 19 29 39 49
[5,] 10 20 30 40 50
>
> ## assignment of whole columns
> tmp3[,1] <- c(1:10*100.0)
> tmp3[,1:2] <- tmp3[,1:2]*100
> tmp3[,1:2] <- tmp3[,2:1]
> tmp3[,1:2]
[,1] [,2]
[1,] 1100 1e+04
[2,] 1200 2e+04
[3,] 1300 3e+04
[4,] 1400 4e+04
[5,] 1500 5e+04
[6,] 1600 6e+04
[7,] 1700 7e+04
[8,] 1800 8e+04
[9,] 1900 9e+04
[10,] 2000 1e+05
>
>
> tmp3[,-1] <- tmp3[,1:9]
> tmp3[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1100 1100 1e+04 21 31 41 51 61 71 81
[2,] 1200 1200 2e+04 22 32 42 52 62 72 82
[3,] 1300 1300 3e+04 23 33 43 53 63 73 83
[4,] 1400 1400 4e+04 24 34 44 54 64 74 84
[5,] 1500 1500 5e+04 25 35 45 55 65 75 85
[6,] 1600 1600 6e+04 26 36 46 56 66 76 86
[7,] 1700 1700 7e+04 27 37 47 57 67 77 87
[8,] 1800 1800 8e+04 28 38 48 58 68 78 88
[9,] 1900 1900 9e+04 29 39 49 59 69 79 89
[10,] 2000 2000 1e+05 30 40 50 60 70 80 90
>
> tmp3[,1:2] <- rep(1,10)
> tmp3[,1:2] <- rep(1,20)
> tmp3[,1:2] <- matrix(c(1:5),1,5)
>
> tmp3[,-c(1:8)] <- matrix(c(1:5),1,5)
>
> tmp3[1,] <- 1:10
> tmp3[1,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
> tmp3[-1,] <- c(1,2)
> tmp3[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
[2,] 1 2 1 2 1 2 1 2 1 2
[3,] 2 1 2 1 2 1 2 1 2 1
[4,] 1 2 1 2 1 2 1 2 1 2
[5,] 2 1 2 1 2 1 2 1 2 1
[6,] 1 2 1 2 1 2 1 2 1 2
[7,] 2 1 2 1 2 1 2 1 2 1
[8,] 1 2 1 2 1 2 1 2 1 2
[9,] 2 1 2 1 2 1 2 1 2 1
[10,] 1 2 1 2 1 2 1 2 1 2
> tmp3[-c(1:8),] <- matrix(c(1:5),1,5)
> tmp3[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
[2,] 1 2 1 2 1 2 1 2 1 2
[3,] 2 1 2 1 2 1 2 1 2 1
[4,] 1 2 1 2 1 2 1 2 1 2
[5,] 2 1 2 1 2 1 2 1 2 1
[6,] 1 2 1 2 1 2 1 2 1 2
[7,] 2 1 2 1 2 1 2 1 2 1
[8,] 1 2 1 2 1 2 1 2 1 2
[9,] 1 3 5 2 4 1 3 5 2 4
[10,] 2 4 1 3 5 2 4 1 3 5
>
>
> tmp3[1:2,1:2] <- 5555.04
> tmp3[-(1:2),1:2] <- 1234.56789
>
>
>
> ## testing accessors for the directory and prefix
> directory(tmp3)
[1] "/Users/biocbuild/bbs-3.9-bioc/meat/BufferedMatrix.Rcheck/tests"
> prefix(tmp3)
[1] "BM"
>
> ## testing if we can remove these objects
> rm(tmp, tmp2, tmp3)
> gc()
used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
Ncells 413935 22.2 873778 46.7 NA 617785 33.0
Vcells 743535 5.7 8388608 64.0 65536 1814644 13.9
>
>
>
>
> ##
> ## 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] "Mon Apr 8 23:37:03 2019"
> 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] "Mon Apr 8 23:37:03 2019"
>
>
> 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: 0x7f8924f31660>
>
>
>
> 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] "Mon Apr 8 23:37:06 2019"
> 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] "Mon Apr 8 23:37:06 2019"
>
> ColMode(tmp2)
<pointer: 0x7f8924f31660>
>
>
>
> ### 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,] 100.4418130 0.7749462 1.7270268 -0.7309753
[2,] 0.4111563 2.0999978 -1.1393420 0.3819790
[3,] 0.4092103 0.1503174 -1.5758043 1.6999574
[4,] 0.2916226 1.9990947 -0.1282571 -0.2058364
> ewApply(tmp5,abs)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.9-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 100.4418130 0.7749462 1.7270268 0.7309753
[2,] 0.4111563 2.0999978 1.1393420 0.3819790
[3,] 0.4092103 0.1503174 1.5758043 1.6999574
[4,] 0.2916226 1.9990947 0.1282571 0.2058364
> ewApply(tmp5,sqrt)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.9-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 10.0220663 0.8803103 1.314164 0.8549709
[2,] 0.6412147 1.4491369 1.067400 0.6180445
[3,] 0.6396955 0.3877079 1.255310 1.3038241
[4,] 0.5400209 1.4138935 0.358130 0.4536919
>
> my.function <- function(x,power){
+ (x+5)^power
+ }
>
> ewApply(tmp5,my.function,power=2)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.9-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 225.66248 34.57805 39.86867 34.28068
[2,] 31.82330 41.59137 36.81334 31.56242
[3,] 31.80617 29.02740 39.12891 39.73820
[4,] 30.69183 41.13803 28.70956 29.74276
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x7f892f10c5b0>
> exp(tmp5)
<pointer: 0x7f892f10c5b0>
> log(tmp5,2)
<pointer: 0x7f892f10c5b0>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 469.6869
> Min(tmp5)
[1] 54.19513
> mean(tmp5)
[1] 72.90323
> Sum(tmp5)
[1] 14580.65
> Var(tmp5)
[1] 849.0578
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 92.01564 72.74223 69.60116 70.10906 68.40834 70.98576 69.11489 71.30333
[9] 73.67817 71.07367
> rowSums(tmp5)
[1] 1840.313 1454.845 1392.023 1402.181 1368.167 1419.715 1382.298 1426.067
[9] 1473.563 1421.473
> rowVars(tmp5)
[1] 7994.29977 59.73964 49.80178 66.25200 57.57659 52.24282
[7] 38.72702 36.08519 41.19795 45.51270
> rowSd(tmp5)
[1] 89.410848 7.729142 7.057038 8.139533 7.587924 7.227919 6.223104
[8] 6.007095 6.418563 6.746310
> rowMax(tmp5)
[1] 469.68688 86.56698 82.70985 85.62342 86.15114 81.27084 85.91405
[8] 80.59460 87.85096 86.05036
> rowMin(tmp5)
[1] 54.26042 61.87669 59.89257 59.75518 54.19513 56.28150 56.38669 59.17862
[9] 61.98525 61.60020
>
> colMeans(tmp5)
[1] 108.06520 75.45394 70.52420 68.93971 70.57525 70.83964 70.12528
[8] 75.28683 69.53216 74.47129 70.50568 71.36073 69.94721 72.28243
[15] 68.69396 70.40601 66.90538 72.15751 71.50516 70.48696
> colSums(tmp5)
[1] 1080.6520 754.5394 705.2420 689.3971 705.7525 708.3964 701.2528
[8] 752.8683 695.3216 744.7129 705.0568 713.6073 699.4721 722.8243
[15] 686.9396 704.0601 669.0538 721.5751 715.0516 704.8696
> colVars(tmp5)
[1] 16150.07084 56.51100 61.30370 88.02951 44.30641 78.18925
[7] 21.71967 30.57213 94.06265 38.57468 83.73186 67.10916
[13] 25.97497 40.89930 59.10019 31.93168 61.32268 79.51014
[19] 70.63129 49.31834
> colSd(tmp5)
[1] 127.082929 7.517380 7.829668 9.382404 6.656306 8.842468
[7] 4.660437 5.529207 9.698590 6.210852 9.150511 8.192018
[13] 5.096564 6.395256 7.687665 5.650812 7.830880 8.916846
[19] 8.404242 7.022702
> colMax(tmp5)
[1] 469.68688 86.56698 82.98140 82.70985 78.27728 87.85096 74.46983
[8] 81.76643 86.15114 84.37214 85.91405 85.40917 80.13591 81.55796
[15] 81.27084 79.26235 80.13681 86.49559 86.05036 84.21809
> colMin(tmp5)
[1] 63.88103 60.41672 59.75518 54.19513 56.38669 57.99019 60.86463 64.20413
[9] 55.98345 65.47710 61.04256 59.17862 63.82455 62.98914 54.26042 61.66364
[17] 55.46596 56.28150 59.48263 61.60020
>
>
> ### setting a random element to NA and then testing with na.rm=TRUE or na.rm=FALSE (The default)
>
>
> which.row <- sample(1:10,1,replace=TRUE)
> which.col <- sample(1:20,1,replace=TRUE)
>
> tmp5[which.row,which.col] <- NA
>
> Max(tmp5)
[1] NA
> Min(tmp5)
[1] NA
> mean(tmp5)
[1] NA
> Sum(tmp5)
[1] NA
> Var(tmp5)
[1] NA
>
> rowMeans(tmp5)
[1] 92.01564 72.74223 69.60116 70.10906 68.40834 70.98576 69.11489 NA
[9] 73.67817 71.07367
> rowSums(tmp5)
[1] 1840.313 1454.845 1392.023 1402.181 1368.167 1419.715 1382.298 NA
[9] 1473.563 1421.473
> rowVars(tmp5)
[1] 7994.29977 59.73964 49.80178 66.25200 57.57659 52.24282
[7] 38.72702 37.80132 41.19795 45.51270
> rowSd(tmp5)
[1] 89.410848 7.729142 7.057038 8.139533 7.587924 7.227919 6.223104
[8] 6.148278 6.418563 6.746310
> rowMax(tmp5)
[1] 469.68688 86.56698 82.70985 85.62342 86.15114 81.27084 85.91405
[8] NA 87.85096 86.05036
> rowMin(tmp5)
[1] 54.26042 61.87669 59.89257 59.75518 54.19513 56.28150 56.38669 NA
[9] 61.98525 61.60020
>
> colMeans(tmp5)
[1] 108.06520 75.45394 70.52420 68.93971 70.57525 70.83964 70.12528
[8] 75.28683 69.53216 74.47129 70.50568 71.36073 69.94721 72.28243
[15] NA 70.40601 66.90538 72.15751 71.50516 70.48696
> colSums(tmp5)
[1] 1080.6520 754.5394 705.2420 689.3971 705.7525 708.3964 701.2528
[8] 752.8683 695.3216 744.7129 705.0568 713.6073 699.4721 722.8243
[15] NA 704.0601 669.0538 721.5751 715.0516 704.8696
> colVars(tmp5)
[1] 16150.07084 56.51100 61.30370 88.02951 44.30641 78.18925
[7] 21.71967 30.57213 94.06265 38.57468 83.73186 67.10916
[13] 25.97497 40.89930 NA 31.93168 61.32268 79.51014
[19] 70.63129 49.31834
> colSd(tmp5)
[1] 127.082929 7.517380 7.829668 9.382404 6.656306 8.842468
[7] 4.660437 5.529207 9.698590 6.210852 9.150511 8.192018
[13] 5.096564 6.395256 NA 5.650812 7.830880 8.916846
[19] 8.404242 7.022702
> colMax(tmp5)
[1] 469.68688 86.56698 82.98140 82.70985 78.27728 87.85096 74.46983
[8] 81.76643 86.15114 84.37214 85.91405 85.40917 80.13591 81.55796
[15] NA 79.26235 80.13681 86.49559 86.05036 84.21809
> colMin(tmp5)
[1] 63.88103 60.41672 59.75518 54.19513 56.38669 57.99019 60.86463 64.20413
[9] 55.98345 65.47710 61.04256 59.17862 63.82455 62.98914 NA 61.66364
[17] 55.46596 56.28150 59.48263 61.60020
>
> Max(tmp5,na.rm=TRUE)
[1] 469.6869
> Min(tmp5,na.rm=TRUE)
[1] 54.19513
> mean(tmp5,na.rm=TRUE)
[1] 72.92243
> Sum(tmp5,na.rm=TRUE)
[1] 14511.56
> Var(tmp5,na.rm=TRUE)
[1] 853.2718
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 92.01564 72.74223 69.60116 70.10906 68.40834 70.98576 69.11489 71.42025
[9] 73.67817 71.07367
> rowSums(tmp5,na.rm=TRUE)
[1] 1840.313 1454.845 1392.023 1402.181 1368.167 1419.715 1382.298 1356.985
[9] 1473.563 1421.473
> rowVars(tmp5,na.rm=TRUE)
[1] 7994.29977 59.73964 49.80178 66.25200 57.57659 52.24282
[7] 38.72702 37.80132 41.19795 45.51270
> rowSd(tmp5,na.rm=TRUE)
[1] 89.410848 7.729142 7.057038 8.139533 7.587924 7.227919 6.223104
[8] 6.148278 6.418563 6.746310
> rowMax(tmp5,na.rm=TRUE)
[1] 469.68688 86.56698 82.70985 85.62342 86.15114 81.27084 85.91405
[8] 80.59460 87.85096 86.05036
> rowMin(tmp5,na.rm=TRUE)
[1] 54.26042 61.87669 59.89257 59.75518 54.19513 56.28150 56.38669 59.17862
[9] 61.98525 61.60020
>
> colMeans(tmp5,na.rm=TRUE)
[1] 108.06520 75.45394 70.52420 68.93971 70.57525 70.83964 70.12528
[8] 75.28683 69.53216 74.47129 70.50568 71.36073 69.94721 72.28243
[15] 68.65086 70.40601 66.90538 72.15751 71.50516 70.48696
> colSums(tmp5,na.rm=TRUE)
[1] 1080.6520 754.5394 705.2420 689.3971 705.7525 708.3964 701.2528
[8] 752.8683 695.3216 744.7129 705.0568 713.6073 699.4721 722.8243
[15] 617.8577 704.0601 669.0538 721.5751 715.0516 704.8696
> colVars(tmp5,na.rm=TRUE)
[1] 16150.07084 56.51100 61.30370 88.02951 44.30641 78.18925
[7] 21.71967 30.57213 94.06265 38.57468 83.73186 67.10916
[13] 25.97497 40.89930 66.46681 31.93168 61.32268 79.51014
[19] 70.63129 49.31834
> colSd(tmp5,na.rm=TRUE)
[1] 127.082929 7.517380 7.829668 9.382404 6.656306 8.842468
[7] 4.660437 5.529207 9.698590 6.210852 9.150511 8.192018
[13] 5.096564 6.395256 8.152718 5.650812 7.830880 8.916846
[19] 8.404242 7.022702
> colMax(tmp5,na.rm=TRUE)
[1] 469.68688 86.56698 82.98140 82.70985 78.27728 87.85096 74.46983
[8] 81.76643 86.15114 84.37214 85.91405 85.40917 80.13591 81.55796
[15] 81.27084 79.26235 80.13681 86.49559 86.05036 84.21809
> colMin(tmp5,na.rm=TRUE)
[1] 63.88103 60.41672 59.75518 54.19513 56.38669 57.99019 60.86463 64.20413
[9] 55.98345 65.47710 61.04256 59.17862 63.82455 62.98914 54.26042 61.66364
[17] 55.46596 56.28150 59.48263 61.60020
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 92.01564 72.74223 69.60116 70.10906 68.40834 70.98576 69.11489 NaN
[9] 73.67817 71.07367
> rowSums(tmp5,na.rm=TRUE)
[1] 1840.313 1454.845 1392.023 1402.181 1368.167 1419.715 1382.298 0.000
[9] 1473.563 1421.473
> rowVars(tmp5,na.rm=TRUE)
[1] 7994.29977 59.73964 49.80178 66.25200 57.57659 52.24282
[7] 38.72702 NA 41.19795 45.51270
> rowSd(tmp5,na.rm=TRUE)
[1] 89.410848 7.729142 7.057038 8.139533 7.587924 7.227919 6.223104
[8] NA 6.418563 6.746310
> rowMax(tmp5,na.rm=TRUE)
[1] 469.68688 86.56698 82.70985 85.62342 86.15114 81.27084 85.91405
[8] NA 87.85096 86.05036
> rowMin(tmp5,na.rm=TRUE)
[1] 54.26042 61.87669 59.89257 59.75518 54.19513 56.28150 56.38669 NA
[9] 61.98525 61.60020
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 112.21430 75.51407 70.78854 68.00357 69.71971 71.19543 71.15424
[8] 75.40307 68.30300 75.02898 71.31274 72.71430 70.25360 71.61309
[15] NaN 70.18160 66.81558 71.61067 71.05759 70.08491
> colSums(tmp5,na.rm=TRUE)
[1] 1009.9287 679.6266 637.0968 612.0321 627.4774 640.7589 640.3882
[8] 678.6277 614.7270 675.2608 641.8147 654.4287 632.2824 644.5178
[15] 0.0000 631.6344 601.3402 644.4960 639.5183 630.7642
> colVars(tmp5,na.rm=TRUE)
[1] 17975.16081 63.53420 68.18059 89.17426 41.61023 86.53884
[7] 12.52357 34.24163 88.82359 39.89756 86.87053 54.88617
[13] 28.16575 40.97148 NA 35.35660 68.89730 86.08478
[19] 77.20657 53.66462
> colSd(tmp5,na.rm=TRUE)
[1] 134.071476 7.970834 8.257154 9.443212 6.450599 9.302625
[7] 3.538866 5.851635 9.424627 6.316452 9.320436 7.408520
[13] 5.307141 6.400897 NA 5.946142 8.300440 9.278188
[19] 8.786727 7.325614
> colMax(tmp5,na.rm=TRUE)
[1] 469.68688 86.56698 82.98140 82.70985 78.27728 87.85096 74.46983
[8] 81.76643 86.15114 84.37214 85.91405 85.40917 80.13591 81.55796
[15] -Inf 79.26235 80.13681 86.49559 86.05036 84.21809
> colMin(tmp5,na.rm=TRUE)
[1] 63.88103 60.41672 59.75518 54.19513 56.38669 57.99019 64.67742 64.20413
[9] 55.98345 65.47710 61.04256 63.93780 63.82455 62.98914 Inf 61.66364
[17] 55.46596 56.28150 59.48263 61.60020
>
>
>
>
> 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] 305.6357 389.0573 297.3821 190.1299 103.8058 242.2817 161.3228 356.5037
[9] 241.3062 288.0597
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 305.6357 389.0573 297.3821 190.1299 103.8058 242.2817 161.3228 356.5037
[9] 241.3062 288.0597
>
>
>
> copymatrix <- matrix(rnorm(200,150,15),10,20)
>
> tmp5[1:10,1:20] <- copymatrix
> which.row <- 1
> which.col <- 3
> cat(which.row," ",which.col,"\n")
1 3
> tmp5[which.row,which.col] <- NA
> copymatrix[which.row,which.col] <- NA
>
> colVars(tmp5,na.rm=TRUE)-apply(copymatrix,2,var,na.rm=TRUE)
[1] 5.684342e-14 1.421085e-14 2.842171e-14 -1.136868e-13 1.136868e-13
[6] 2.842171e-14 2.273737e-13 -1.421085e-14 0.000000e+00 5.684342e-14
[11] -5.684342e-14 -1.705303e-13 -8.526513e-14 0.000000e+00 -1.989520e-13
[16] -1.989520e-13 0.000000e+00 -3.979039e-13 -1.705303e-13 5.684342e-14
>
>
>
>
>
>
>
>
>
>
> ## making sure these things agree
> ##
> ## first when there is no NA
>
>
>
> agree.checks <- function(buff.matrix,r.matrix,err.tol=1e-10){
+
+ if (Max(buff.matrix,na.rm=TRUE) != max(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Max")
+ }
+
+
+ if (Min(buff.matrix,na.rm=TRUE) != min(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Min")
+ }
+
+
+ if (abs(Sum(buff.matrix,na.rm=TRUE)- sum(r.matrix,na.rm=TRUE)) > err.tol){
+
+ cat(Sum(buff.matrix,na.rm=TRUE),"\n")
+ cat(sum(r.matrix,na.rm=TRUE),"\n")
+ cat(Sum(buff.matrix,na.rm=TRUE) - sum(r.matrix,na.rm=TRUE),"\n")
+
+ stop("No agreement in Sum")
+ }
+
+ if (abs(mean(buff.matrix,na.rm=TRUE) - mean(r.matrix,na.rm=TRUE)) > err.tol){
+ stop("No agreement in mean")
+ }
+
+
+ if(abs(Var(buff.matrix,na.rm=TRUE) - var(as.vector(r.matrix),na.rm=TRUE)) > err.tol){
+ stop("No agreement in Var")
+ }
+
+
+
+ if(any(abs(rowMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,mean,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowMeans")
+ }
+
+
+ if(any(abs(colMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,mean,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colMeans")
+ }
+
+
+ if(any(abs(rowSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in rowSums")
+ }
+
+
+ if(any(abs(colSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colSums")
+ }
+
+ ### this is to get around the fact that R doesn't like to compute NA on an entire vector of NA when
+ ### computing variance
+ my.Var <- function(x,na.rm=FALSE){
+ if (all(is.na(x))){
+ return(NA)
+ } else {
+ var(x,na.rm=na.rm)
+ }
+
+ }
+
+ if(any(abs(rowVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(colVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(rowMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+ if(any(abs(colMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+
+ if(any(abs(rowMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+
+ if(any(abs(colMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+ if(any(abs(colMedians(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,median,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMedian")
+ }
+
+ if(any(abs(colRanges(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,range,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colRanges")
+ }
+
+
+
+ }
>
>
>
>
>
>
>
>
>
> for (rep in 1:20){
+ copymatrix <- matrix(rnorm(200,150,15),10,20)
+
+ tmp5[1:10,1:20] <- copymatrix
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ## now lets assign some NA values and check agreement
+
+ which.row <- sample(1:10,1,replace=TRUE)
+ which.col <- sample(1:20,1,replace=TRUE)
+
+ cat(which.row," ",which.col,"\n")
+
+ tmp5[which.row,which.col] <- NA
+ copymatrix[which.row,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ## make an entire row NA
+ tmp5[which.row,] <- NA
+ copymatrix[which.row,] <- NA
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ### also make an entire col NA
+ tmp5[,which.col] <- NA
+ copymatrix[,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ### now make 1 element non NA with NA in the rest of row and column
+
+ tmp5[which.row,which.col] <- rnorm(1,150,15)
+ copymatrix[which.row,which.col] <- tmp5[which.row,which.col]
+
+ agree.checks(tmp5,copymatrix)
+ }
8 8
3 2
2 19
1 14
10 12
1 20
7 14
10 13
3 7
4 7
2 2
3 1
8 18
8 19
4 8
6 11
4 7
5 9
7 15
6 15
There were 50 or more warnings (use warnings() to see the first 50)
>
>
> ### now test 1 by n and n by 1 matrix
>
>
> err.tol <- 1e-12
>
> rm(tmp5)
>
> dataset1 <- rnorm(100)
> dataset2 <- rnorm(100)
>
> tmp <- createBufferedMatrix(1,100)
> tmp[1,] <- dataset1
>
> tmp2 <- createBufferedMatrix(100,1)
> tmp2[,1] <- dataset2
>
>
>
>
>
> Max(tmp)
[1] 2.647727
> Min(tmp)
[1] -2.497764
> mean(tmp)
[1] -0.05611939
> Sum(tmp)
[1] -5.611939
> Var(tmp)
[1] 0.8649517
>
> rowMeans(tmp)
[1] -0.05611939
> rowSums(tmp)
[1] -5.611939
> rowVars(tmp)
[1] 0.8649517
> rowSd(tmp)
[1] 0.9300278
> rowMax(tmp)
[1] 2.647727
> rowMin(tmp)
[1] -2.497764
>
> colMeans(tmp)
[1] 0.70133725 -0.40777132 -1.00429177 -0.71841388 -0.23480816 -0.60110739
[7] -0.75615540 0.03508690 -0.81905116 -0.26554019 -0.74958639 1.22188619
[13] -2.01598616 -0.07043171 0.23087320 -1.07518723 0.82389795 0.48882480
[19] -1.42175392 -1.45136314 0.65836116 0.34763442 -0.51645758 0.66419349
[25] 1.16347497 -0.64533148 -0.29292196 0.40264835 1.84893584 -0.13208826
[31] -0.58691205 0.14596012 0.13874365 -0.19784475 2.28322894 -0.99319935
[37] 0.75542828 -0.77961190 -0.94110360 -0.59015243 1.42999932 0.12534867
[43] -2.49776411 -0.31083395 -1.38134889 -0.28667093 -0.79335802 1.38502112
[49] -1.17477560 0.50735826 -0.27893814 -0.26388719 0.92112833 0.38280958
[55] 0.56534283 0.62662336 -1.31627608 0.67478536 1.24829064 -1.54457288
[61] 2.64772710 0.25054993 -1.42423789 0.87557579 0.40552404 0.56780320
[67] 0.22701034 0.86242933 -1.68821900 0.64560396 -1.37365753 -1.00306902
[73] -0.96340390 0.40284726 -0.04765508 0.35325328 -0.55010582 0.93281848
[79] -0.48187830 -0.99082908 0.13990715 -0.56649240 -0.68614305 -0.36997213
[85] -0.37066533 0.42015915 -0.16244483 -0.44482210 0.03347511 0.32228035
[91] 0.52784558 -0.26022682 0.34611891 0.89249853 0.09755376 -0.46028252
[97] 1.34313779 0.02859431 -0.92025774 2.16798467
> colSums(tmp)
[1] 0.70133725 -0.40777132 -1.00429177 -0.71841388 -0.23480816 -0.60110739
[7] -0.75615540 0.03508690 -0.81905116 -0.26554019 -0.74958639 1.22188619
[13] -2.01598616 -0.07043171 0.23087320 -1.07518723 0.82389795 0.48882480
[19] -1.42175392 -1.45136314 0.65836116 0.34763442 -0.51645758 0.66419349
[25] 1.16347497 -0.64533148 -0.29292196 0.40264835 1.84893584 -0.13208826
[31] -0.58691205 0.14596012 0.13874365 -0.19784475 2.28322894 -0.99319935
[37] 0.75542828 -0.77961190 -0.94110360 -0.59015243 1.42999932 0.12534867
[43] -2.49776411 -0.31083395 -1.38134889 -0.28667093 -0.79335802 1.38502112
[49] -1.17477560 0.50735826 -0.27893814 -0.26388719 0.92112833 0.38280958
[55] 0.56534283 0.62662336 -1.31627608 0.67478536 1.24829064 -1.54457288
[61] 2.64772710 0.25054993 -1.42423789 0.87557579 0.40552404 0.56780320
[67] 0.22701034 0.86242933 -1.68821900 0.64560396 -1.37365753 -1.00306902
[73] -0.96340390 0.40284726 -0.04765508 0.35325328 -0.55010582 0.93281848
[79] -0.48187830 -0.99082908 0.13990715 -0.56649240 -0.68614305 -0.36997213
[85] -0.37066533 0.42015915 -0.16244483 -0.44482210 0.03347511 0.32228035
[91] 0.52784558 -0.26022682 0.34611891 0.89249853 0.09755376 -0.46028252
[97] 1.34313779 0.02859431 -0.92025774 2.16798467
> 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] 0.70133725 -0.40777132 -1.00429177 -0.71841388 -0.23480816 -0.60110739
[7] -0.75615540 0.03508690 -0.81905116 -0.26554019 -0.74958639 1.22188619
[13] -2.01598616 -0.07043171 0.23087320 -1.07518723 0.82389795 0.48882480
[19] -1.42175392 -1.45136314 0.65836116 0.34763442 -0.51645758 0.66419349
[25] 1.16347497 -0.64533148 -0.29292196 0.40264835 1.84893584 -0.13208826
[31] -0.58691205 0.14596012 0.13874365 -0.19784475 2.28322894 -0.99319935
[37] 0.75542828 -0.77961190 -0.94110360 -0.59015243 1.42999932 0.12534867
[43] -2.49776411 -0.31083395 -1.38134889 -0.28667093 -0.79335802 1.38502112
[49] -1.17477560 0.50735826 -0.27893814 -0.26388719 0.92112833 0.38280958
[55] 0.56534283 0.62662336 -1.31627608 0.67478536 1.24829064 -1.54457288
[61] 2.64772710 0.25054993 -1.42423789 0.87557579 0.40552404 0.56780320
[67] 0.22701034 0.86242933 -1.68821900 0.64560396 -1.37365753 -1.00306902
[73] -0.96340390 0.40284726 -0.04765508 0.35325328 -0.55010582 0.93281848
[79] -0.48187830 -0.99082908 0.13990715 -0.56649240 -0.68614305 -0.36997213
[85] -0.37066533 0.42015915 -0.16244483 -0.44482210 0.03347511 0.32228035
[91] 0.52784558 -0.26022682 0.34611891 0.89249853 0.09755376 -0.46028252
[97] 1.34313779 0.02859431 -0.92025774 2.16798467
> colMin(tmp)
[1] 0.70133725 -0.40777132 -1.00429177 -0.71841388 -0.23480816 -0.60110739
[7] -0.75615540 0.03508690 -0.81905116 -0.26554019 -0.74958639 1.22188619
[13] -2.01598616 -0.07043171 0.23087320 -1.07518723 0.82389795 0.48882480
[19] -1.42175392 -1.45136314 0.65836116 0.34763442 -0.51645758 0.66419349
[25] 1.16347497 -0.64533148 -0.29292196 0.40264835 1.84893584 -0.13208826
[31] -0.58691205 0.14596012 0.13874365 -0.19784475 2.28322894 -0.99319935
[37] 0.75542828 -0.77961190 -0.94110360 -0.59015243 1.42999932 0.12534867
[43] -2.49776411 -0.31083395 -1.38134889 -0.28667093 -0.79335802 1.38502112
[49] -1.17477560 0.50735826 -0.27893814 -0.26388719 0.92112833 0.38280958
[55] 0.56534283 0.62662336 -1.31627608 0.67478536 1.24829064 -1.54457288
[61] 2.64772710 0.25054993 -1.42423789 0.87557579 0.40552404 0.56780320
[67] 0.22701034 0.86242933 -1.68821900 0.64560396 -1.37365753 -1.00306902
[73] -0.96340390 0.40284726 -0.04765508 0.35325328 -0.55010582 0.93281848
[79] -0.48187830 -0.99082908 0.13990715 -0.56649240 -0.68614305 -0.36997213
[85] -0.37066533 0.42015915 -0.16244483 -0.44482210 0.03347511 0.32228035
[91] 0.52784558 -0.26022682 0.34611891 0.89249853 0.09755376 -0.46028252
[97] 1.34313779 0.02859431 -0.92025774 2.16798467
> colMedians(tmp)
[1] 0.70133725 -0.40777132 -1.00429177 -0.71841388 -0.23480816 -0.60110739
[7] -0.75615540 0.03508690 -0.81905116 -0.26554019 -0.74958639 1.22188619
[13] -2.01598616 -0.07043171 0.23087320 -1.07518723 0.82389795 0.48882480
[19] -1.42175392 -1.45136314 0.65836116 0.34763442 -0.51645758 0.66419349
[25] 1.16347497 -0.64533148 -0.29292196 0.40264835 1.84893584 -0.13208826
[31] -0.58691205 0.14596012 0.13874365 -0.19784475 2.28322894 -0.99319935
[37] 0.75542828 -0.77961190 -0.94110360 -0.59015243 1.42999932 0.12534867
[43] -2.49776411 -0.31083395 -1.38134889 -0.28667093 -0.79335802 1.38502112
[49] -1.17477560 0.50735826 -0.27893814 -0.26388719 0.92112833 0.38280958
[55] 0.56534283 0.62662336 -1.31627608 0.67478536 1.24829064 -1.54457288
[61] 2.64772710 0.25054993 -1.42423789 0.87557579 0.40552404 0.56780320
[67] 0.22701034 0.86242933 -1.68821900 0.64560396 -1.37365753 -1.00306902
[73] -0.96340390 0.40284726 -0.04765508 0.35325328 -0.55010582 0.93281848
[79] -0.48187830 -0.99082908 0.13990715 -0.56649240 -0.68614305 -0.36997213
[85] -0.37066533 0.42015915 -0.16244483 -0.44482210 0.03347511 0.32228035
[91] 0.52784558 -0.26022682 0.34611891 0.89249853 0.09755376 -0.46028252
[97] 1.34313779 0.02859431 -0.92025774 2.16798467
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] 0.7013372 -0.4077713 -1.004292 -0.7184139 -0.2348082 -0.6011074 -0.7561554
[2,] 0.7013372 -0.4077713 -1.004292 -0.7184139 -0.2348082 -0.6011074 -0.7561554
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] 0.0350869 -0.8190512 -0.2655402 -0.7495864 1.221886 -2.015986 -0.07043171
[2,] 0.0350869 -0.8190512 -0.2655402 -0.7495864 1.221886 -2.015986 -0.07043171
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] 0.2308732 -1.075187 0.823898 0.4888248 -1.421754 -1.451363 0.6583612
[2,] 0.2308732 -1.075187 0.823898 0.4888248 -1.421754 -1.451363 0.6583612
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] 0.3476344 -0.5164576 0.6641935 1.163475 -0.6453315 -0.292922 0.4026483
[2,] 0.3476344 -0.5164576 0.6641935 1.163475 -0.6453315 -0.292922 0.4026483
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] 1.848936 -0.1320883 -0.5869121 0.1459601 0.1387436 -0.1978447 2.283229
[2,] 1.848936 -0.1320883 -0.5869121 0.1459601 0.1387436 -0.1978447 2.283229
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] -0.9931993 0.7554283 -0.7796119 -0.9411036 -0.5901524 1.429999 0.1253487
[2,] -0.9931993 0.7554283 -0.7796119 -0.9411036 -0.5901524 1.429999 0.1253487
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] -2.497764 -0.3108339 -1.381349 -0.2866709 -0.793358 1.385021 -1.174776
[2,] -2.497764 -0.3108339 -1.381349 -0.2866709 -0.793358 1.385021 -1.174776
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] 0.5073583 -0.2789381 -0.2638872 0.9211283 0.3828096 0.5653428 0.6266234
[2,] 0.5073583 -0.2789381 -0.2638872 0.9211283 0.3828096 0.5653428 0.6266234
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] -1.316276 0.6747854 1.248291 -1.544573 2.647727 0.2505499 -1.424238
[2,] -1.316276 0.6747854 1.248291 -1.544573 2.647727 0.2505499 -1.424238
[,64] [,65] [,66] [,67] [,68] [,69] [,70]
[1,] 0.8755758 0.405524 0.5678032 0.2270103 0.8624293 -1.688219 0.645604
[2,] 0.8755758 0.405524 0.5678032 0.2270103 0.8624293 -1.688219 0.645604
[,71] [,72] [,73] [,74] [,75] [,76] [,77]
[1,] -1.373658 -1.003069 -0.9634039 0.4028473 -0.04765508 0.3532533 -0.5501058
[2,] -1.373658 -1.003069 -0.9634039 0.4028473 -0.04765508 0.3532533 -0.5501058
[,78] [,79] [,80] [,81] [,82] [,83] [,84]
[1,] 0.9328185 -0.4818783 -0.9908291 0.1399072 -0.5664924 -0.6861431 -0.3699721
[2,] 0.9328185 -0.4818783 -0.9908291 0.1399072 -0.5664924 -0.6861431 -0.3699721
[,85] [,86] [,87] [,88] [,89] [,90] [,91]
[1,] -0.3706653 0.4201592 -0.1624448 -0.4448221 0.03347511 0.3222803 0.5278456
[2,] -0.3706653 0.4201592 -0.1624448 -0.4448221 0.03347511 0.3222803 0.5278456
[,92] [,93] [,94] [,95] [,96] [,97] [,98]
[1,] -0.2602268 0.3461189 0.8924985 0.09755376 -0.4602825 1.343138 0.02859431
[2,] -0.2602268 0.3461189 0.8924985 0.09755376 -0.4602825 1.343138 0.02859431
[,99] [,100]
[1,] -0.9202577 2.167985
[2,] -0.9202577 2.167985
>
>
> Max(tmp2)
[1] 2.203208
> Min(tmp2)
[1] -1.989466
> mean(tmp2)
[1] -0.1045287
> Sum(tmp2)
[1] -10.45287
> Var(tmp2)
[1] 0.7616532
>
> rowMeans(tmp2)
[1] -1.246119346 -0.538502553 0.848156578 0.392506646 -0.181517739
[6] -0.437539817 -0.299053489 -0.951381088 -0.539692003 -0.209918984
[11] -0.263471382 -0.558312310 -1.167676136 -0.491709893 -0.348903028
[16] -1.086709481 0.564072777 0.133258377 -0.478832120 0.800783753
[21] -0.078233757 0.618079753 -1.058892189 0.444263089 -0.611559712
[26] -0.645604008 -0.447428950 0.847336223 1.524109137 -0.845954152
[31] -0.051143692 1.001767778 0.318390988 -0.489215849 0.322579533
[36] 1.229758657 -1.989466070 -0.732554010 0.212623980 -0.360735419
[41] 0.890532053 -0.506608797 -0.611297458 -0.990211480 2.203208192
[46] -1.307079536 -0.410754290 -0.864232132 -0.063980158 -0.364133690
[51] -0.096725554 0.374084813 0.107064382 1.435587224 -0.760048230
[56] -1.943224989 0.267564292 0.098488502 -1.077809701 -1.391920732
[61] -1.892234148 0.329318942 0.007681211 0.949428115 -0.936186506
[66] -0.413450122 -1.184284759 -1.177488768 0.368647003 -0.519957743
[71] -0.710070673 1.403705863 1.649180804 0.426829578 -0.029215974
[76] 1.243112816 1.938985399 -0.553624034 1.439304313 -1.391468320
[81] 0.178501031 0.218723813 -0.604705045 -0.118855718 -0.019810092
[86] -0.781758410 -0.324030586 -0.714407427 0.701071365 1.298079353
[91] -1.038014180 0.872405426 0.351210810 0.783905223 1.048369836
[96] 0.361407387 0.252018474 0.136969465 -1.091408661 -1.046814373
> rowSums(tmp2)
[1] -1.246119346 -0.538502553 0.848156578 0.392506646 -0.181517739
[6] -0.437539817 -0.299053489 -0.951381088 -0.539692003 -0.209918984
[11] -0.263471382 -0.558312310 -1.167676136 -0.491709893 -0.348903028
[16] -1.086709481 0.564072777 0.133258377 -0.478832120 0.800783753
[21] -0.078233757 0.618079753 -1.058892189 0.444263089 -0.611559712
[26] -0.645604008 -0.447428950 0.847336223 1.524109137 -0.845954152
[31] -0.051143692 1.001767778 0.318390988 -0.489215849 0.322579533
[36] 1.229758657 -1.989466070 -0.732554010 0.212623980 -0.360735419
[41] 0.890532053 -0.506608797 -0.611297458 -0.990211480 2.203208192
[46] -1.307079536 -0.410754290 -0.864232132 -0.063980158 -0.364133690
[51] -0.096725554 0.374084813 0.107064382 1.435587224 -0.760048230
[56] -1.943224989 0.267564292 0.098488502 -1.077809701 -1.391920732
[61] -1.892234148 0.329318942 0.007681211 0.949428115 -0.936186506
[66] -0.413450122 -1.184284759 -1.177488768 0.368647003 -0.519957743
[71] -0.710070673 1.403705863 1.649180804 0.426829578 -0.029215974
[76] 1.243112816 1.938985399 -0.553624034 1.439304313 -1.391468320
[81] 0.178501031 0.218723813 -0.604705045 -0.118855718 -0.019810092
[86] -0.781758410 -0.324030586 -0.714407427 0.701071365 1.298079353
[91] -1.038014180 0.872405426 0.351210810 0.783905223 1.048369836
[96] 0.361407387 0.252018474 0.136969465 -1.091408661 -1.046814373
> 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] -1.246119346 -0.538502553 0.848156578 0.392506646 -0.181517739
[6] -0.437539817 -0.299053489 -0.951381088 -0.539692003 -0.209918984
[11] -0.263471382 -0.558312310 -1.167676136 -0.491709893 -0.348903028
[16] -1.086709481 0.564072777 0.133258377 -0.478832120 0.800783753
[21] -0.078233757 0.618079753 -1.058892189 0.444263089 -0.611559712
[26] -0.645604008 -0.447428950 0.847336223 1.524109137 -0.845954152
[31] -0.051143692 1.001767778 0.318390988 -0.489215849 0.322579533
[36] 1.229758657 -1.989466070 -0.732554010 0.212623980 -0.360735419
[41] 0.890532053 -0.506608797 -0.611297458 -0.990211480 2.203208192
[46] -1.307079536 -0.410754290 -0.864232132 -0.063980158 -0.364133690
[51] -0.096725554 0.374084813 0.107064382 1.435587224 -0.760048230
[56] -1.943224989 0.267564292 0.098488502 -1.077809701 -1.391920732
[61] -1.892234148 0.329318942 0.007681211 0.949428115 -0.936186506
[66] -0.413450122 -1.184284759 -1.177488768 0.368647003 -0.519957743
[71] -0.710070673 1.403705863 1.649180804 0.426829578 -0.029215974
[76] 1.243112816 1.938985399 -0.553624034 1.439304313 -1.391468320
[81] 0.178501031 0.218723813 -0.604705045 -0.118855718 -0.019810092
[86] -0.781758410 -0.324030586 -0.714407427 0.701071365 1.298079353
[91] -1.038014180 0.872405426 0.351210810 0.783905223 1.048369836
[96] 0.361407387 0.252018474 0.136969465 -1.091408661 -1.046814373
> rowMin(tmp2)
[1] -1.246119346 -0.538502553 0.848156578 0.392506646 -0.181517739
[6] -0.437539817 -0.299053489 -0.951381088 -0.539692003 -0.209918984
[11] -0.263471382 -0.558312310 -1.167676136 -0.491709893 -0.348903028
[16] -1.086709481 0.564072777 0.133258377 -0.478832120 0.800783753
[21] -0.078233757 0.618079753 -1.058892189 0.444263089 -0.611559712
[26] -0.645604008 -0.447428950 0.847336223 1.524109137 -0.845954152
[31] -0.051143692 1.001767778 0.318390988 -0.489215849 0.322579533
[36] 1.229758657 -1.989466070 -0.732554010 0.212623980 -0.360735419
[41] 0.890532053 -0.506608797 -0.611297458 -0.990211480 2.203208192
[46] -1.307079536 -0.410754290 -0.864232132 -0.063980158 -0.364133690
[51] -0.096725554 0.374084813 0.107064382 1.435587224 -0.760048230
[56] -1.943224989 0.267564292 0.098488502 -1.077809701 -1.391920732
[61] -1.892234148 0.329318942 0.007681211 0.949428115 -0.936186506
[66] -0.413450122 -1.184284759 -1.177488768 0.368647003 -0.519957743
[71] -0.710070673 1.403705863 1.649180804 0.426829578 -0.029215974
[76] 1.243112816 1.938985399 -0.553624034 1.439304313 -1.391468320
[81] 0.178501031 0.218723813 -0.604705045 -0.118855718 -0.019810092
[86] -0.781758410 -0.324030586 -0.714407427 0.701071365 1.298079353
[91] -1.038014180 0.872405426 0.351210810 0.783905223 1.048369836
[96] 0.361407387 0.252018474 0.136969465 -1.091408661 -1.046814373
>
> colMeans(tmp2)
[1] -0.1045287
> colSums(tmp2)
[1] -10.45287
> colVars(tmp2)
[1] 0.7616532
> colSd(tmp2)
[1] 0.8727274
> colMax(tmp2)
[1] 2.203208
> colMin(tmp2)
[1] -1.989466
> colMedians(tmp2)
[1] -0.1957184
> colRanges(tmp2)
[,1]
[1,] -1.989466
[2,] 2.203208
>
> dataset1 <- matrix(dataset1,1,100)
>
> agree.checks(tmp,dataset1)
>
> dataset2 <- matrix(dataset2,100,1)
> agree.checks(tmp2,dataset2)
>
>
> tmp <- createBufferedMatrix(10,10)
>
> tmp[1:10,1:10] <- rnorm(100)
> colApply(tmp,sum)
[1] 3.7435006 -2.1477798 1.0164516 -1.9415310 -1.2177311 -0.4014171
[7] 2.4902348 -1.6897083 5.2897796 2.8124478
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.0694057
[2,] -0.5931699
[3,] 0.2463144
[4,] 1.2952339
[5,] 2.2089091
>
> rowApply(tmp,sum)
[1] 1.8192624 2.7966328 -4.0775164 -0.4386734 -0.1286272 2.9410528
[7] 4.2568362 -1.2101038 -1.2797488 3.2751324
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 9 1 9 9 2 6 10 2 3 10
[2,] 1 3 2 8 6 1 3 4 9 6
[3,] 8 8 4 4 3 4 5 8 2 8
[4,] 3 5 7 10 1 3 2 5 4 3
[5,] 4 9 3 2 10 8 1 6 6 5
[6,] 2 10 1 6 5 10 8 7 8 1
[7,] 7 7 6 7 9 7 4 3 7 9
[8,] 5 4 8 1 4 9 7 1 5 2
[9,] 6 2 10 5 7 5 6 9 10 7
[10,] 10 6 5 3 8 2 9 10 1 4
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] -0.12515034 -1.73380090 -1.79624735 -4.06808943 0.02638786 -0.63926070
[7] -1.50128614 2.81201274 -1.33212503 -0.38046966 -2.76864075 -4.38110388
[13] -1.52045469 1.44587538 0.45456018 -0.04513469 0.96882239 -2.12436546
[19] 2.15854710 -3.39197956
> colApply(tmp,quantile)[,1]
[,1]
[1,] -0.87157162
[2,] -0.22816517
[3,] -0.02337471
[4,] 0.29376034
[5,] 0.70420081
>
> rowApply(tmp,sum)
[1] 0.03607194 -3.46794397 -9.57752021 0.29720088 -5.22971158
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 3 13 12 8 18
[2,] 18 3 14 9 8
[3,] 14 1 9 20 7
[4,] 16 8 5 12 1
[5,] 5 2 20 16 15
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] -0.87157162 0.574996971 0.2878195 0.5076669 -0.3964465 0.17104765
[2,] 0.29376034 -1.510843694 -2.4448241 -0.5970120 -1.8542813 0.09397473
[3,] -0.22816517 -0.168841910 -0.7579470 -1.0487061 1.1993707 -0.91082540
[4,] -0.02337471 -0.003778279 1.8335853 0.1746241 0.5226431 -0.33312496
[5,] 0.70420081 -0.625333985 -0.7148810 -3.1046625 0.5551018 0.33966729
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] 0.09952057 -0.4726213 0.52561824 -1.52911028 0.02647617 -0.901099454
[2,] -0.69103393 1.8432974 0.05197919 1.04428126 -0.99818231 -0.584713579
[3,] -1.61542498 0.6931361 -0.68933001 -0.23821110 -2.15658109 -0.003874103
[4,] 0.01733353 -0.7352707 -0.89491202 0.29306683 1.77125353 -2.557398914
[5,] 0.68831867 1.4834712 -0.32548043 0.04950363 -1.41160705 -0.334017827
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] 0.03099256 0.90170044 -0.2601461 -0.1485225 0.4511155 0.1495624
[2,] 1.04342900 -0.32539004 1.2317662 0.3068028 -1.3393014 1.2788635
[3,] -0.19380883 0.48916804 0.1804352 -1.1127934 -0.8449955 -1.8703538
[4,] -1.40541291 0.08175718 0.4646413 0.3073661 1.6648366 -0.7043058
[5,] -0.99565451 0.29863977 -1.1621364 0.6020122 1.0371672 -0.9781317
[,19] [,20]
[1,] 1.0995837 -0.2105109
[2,] 0.7974085 -1.1079244
[3,] -0.7780995 0.4783276
[4,] 0.6946984 -0.8710268
[5,] 0.3449560 -1.6808450
>
>
> is.BufferedMatrix(tmp)
[1] TRUE
>
> as.BufferedMatrix(as.matrix(tmp))
BufferedMatrix object
Matrix size: 5 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.9-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 800 bytes.
>
>
>
> subBufferedMatrix(tmp,1:5,1:5)
BufferedMatrix object
Matrix size: 5 5
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.9-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 644 bytes.
Disk usage : 200 bytes.
> subBufferedMatrix(tmp,,5:8)
BufferedMatrix object
Matrix size: 5 4
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.9-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 557 bytes.
Disk usage : 160 bytes.
> subBufferedMatrix(tmp,1:3,)
BufferedMatrix object
Matrix size: 3 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.9-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 1.608951 -1.370022 1.660997 1.002864 -0.7275521 0.2777787 1.118884
col8 col9 col10 col11 col12 col13 col14
row1 -0.6212624 -1.07825 0.3722482 0.1145722 0.7292831 1.68435 -0.5700924
col15 col16 col17 col18 col19 col20
row1 1.267829 -1.958232 1.426565 0.1436162 -0.3008122 0.736084
> tmp[,"col10"]
col10
row1 0.37224821
row2 -0.49394693
row3 0.81018100
row4 -0.94062162
row5 0.09940407
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7
row1 1.608951 -1.3700224 1.660997 1.002864 -0.7275521 0.2777787 1.1188837
row5 -1.114342 -0.2982367 -1.337582 1.086744 0.4521023 -0.1088653 -0.5164682
col8 col9 col10 col11 col12 col13
row1 -0.6212624 -1.078250 0.37224821 0.11457219 0.7292831 1.684350
row5 -0.5204260 1.052373 0.09940407 -0.09130324 -0.7053640 -1.641222
col14 col15 col16 col17 col18 col19
row1 -0.5700924 1.2678285 -1.9582315 1.4265653 0.1436162 -0.30081221
row5 -0.9331492 -0.7094629 -0.1682138 -0.1711418 -0.7448618 0.04730264
col20
row1 0.736084
row5 1.444865
> tmp[,c("col6","col20")]
col6 col20
row1 0.2777787 0.7360840
row2 -0.9984935 0.3442880
row3 -0.6581536 -1.5618995
row4 1.7204577 -0.9567654
row5 -0.1088653 1.4448650
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 0.2777787 0.736084
row5 -0.1088653 1.444865
>
>
>
>
> 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 52.40225 49.91585 50.86302 48.81336 50.25927 104.4278 49.62519 48.34668
col9 col10 col11 col12 col13 col14 col15 col16
row1 51.52346 49.01566 49.63682 50.47251 51.16666 49.90435 49.88618 50.30792
col17 col18 col19 col20
row1 49.84231 50.26794 49.25969 105.8305
> tmp[,"col10"]
col10
row1 49.01566
row2 30.59438
row3 30.92731
row4 29.90896
row5 50.25807
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 52.40225 49.91585 50.86302 48.81336 50.25927 104.4278 49.62519 48.34668
row5 50.19799 51.17406 47.60965 50.87505 49.06877 105.0635 48.49629 50.18402
col9 col10 col11 col12 col13 col14 col15 col16
row1 51.52346 49.01566 49.63682 50.47251 51.16666 49.90435 49.88618 50.30792
row5 49.89632 50.25807 48.95779 50.26825 50.26867 50.12116 50.42667 50.89429
col17 col18 col19 col20
row1 49.84231 50.26794 49.25969 105.8305
row5 50.13713 49.65043 50.96595 107.5210
> tmp[,c("col6","col20")]
col6 col20
row1 104.42782 105.83052
row2 75.98653 75.40099
row3 75.48813 77.03620
row4 73.75445 73.76151
row5 105.06349 107.52100
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 104.4278 105.8305
row5 105.0635 107.5210
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 104.4278 105.8305
row5 105.0635 107.5210
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] -0.8188854
[2,] -0.8878802
[3,] -1.3135926
[4,] 0.1382827
[5,] 0.4410397
> tmp[,c("col17","col7")]
col17 col7
[1,] 1.6295394 -1.1633516
[2,] 0.5108033 0.6342645
[3,] -2.4823151 0.7173575
[4,] -0.1673356 -0.1496910
[5,] -0.5139743 -0.2632341
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] 0.16058373 -1.54623562
[2,] 0.29627004 0.68505822
[3,] 1.44659303 -0.07404814
[4,] 0.06166562 0.24222426
[5,] 0.77025051 -0.12868570
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] 0.1605837
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] 0.1605837
[2,] 0.2962700
>
>
>
> 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 -0.2776470 0.3545175 0.6552357 -1.011682 -0.3983301 0.33369877
row1 0.2141289 1.5420072 -0.6566408 1.648651 -1.5733495 -0.08690212
[,7] [,8] [,9] [,10] [,11] [,12]
row3 -0.4176531 -0.5630251 1.5717563 -0.336576 -0.5359038 0.04822562
row1 0.8319676 1.8775942 0.3631185 1.046036 -1.4233236 -1.98312729
[,13] [,14] [,15] [,16] [,17] [,18] [,19]
row3 1.0113137 -0.9603006 -0.771252 -1.6930121 0.4682274 2.100416 -0.1968869
row1 -0.6367171 -0.2289892 -0.723986 -0.7230822 -1.0893244 -1.145118 -0.4012154
[,20]
row3 0.8584042
row1 -0.4086115
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 -1.098006 -0.2546677 -0.3697781 1.340667 -0.1836817 0.4822961 1.5079
[,8] [,9] [,10]
row2 2.064078 -0.5112884 1.36588
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6]
row5 -0.6945731 -0.04759507 -0.1757595 -1.318432 -0.8466188 -2.240869
[,7] [,8] [,9] [,10] [,11] [,12] [,13]
row5 -0.4081626 -0.05646753 0.1892649 -1.841017 0.4444189 -1.470957 1.137033
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
row5 -0.4210993 1.554703 0.4734264 1.54105 -0.1730304 -0.7133994 -1.249891
>
>
> 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: 0x7f8922e29080>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/Users/biocbuild/bbs-3.9-bioc/meat/BufferedMatrix.Rcheck/tests/BMdc5fedec2f4"
[2] "/Users/biocbuild/bbs-3.9-bioc/meat/BufferedMatrix.Rcheck/tests/BMdc5f42d128cc"
[3] "/Users/biocbuild/bbs-3.9-bioc/meat/BufferedMatrix.Rcheck/tests/BMdc5f31cd8b59"
[4] "/Users/biocbuild/bbs-3.9-bioc/meat/BufferedMatrix.Rcheck/tests/BMdc5f2d77999a"
[5] "/Users/biocbuild/bbs-3.9-bioc/meat/BufferedMatrix.Rcheck/tests/BMdc5f70564c8"
[6] "/Users/biocbuild/bbs-3.9-bioc/meat/BufferedMatrix.Rcheck/tests/BMdc5f731b8a11"
[7] "/Users/biocbuild/bbs-3.9-bioc/meat/BufferedMatrix.Rcheck/tests/BMdc5f15059d21"
[8] "/Users/biocbuild/bbs-3.9-bioc/meat/BufferedMatrix.Rcheck/tests/BMdc5f238eec4f"
[9] "/Users/biocbuild/bbs-3.9-bioc/meat/BufferedMatrix.Rcheck/tests/BMdc5f7c3c48c5"
[10] "/Users/biocbuild/bbs-3.9-bioc/meat/BufferedMatrix.Rcheck/tests/BMdc5f59cdbd3b"
[11] "/Users/biocbuild/bbs-3.9-bioc/meat/BufferedMatrix.Rcheck/tests/BMdc5f52429a8c"
[12] "/Users/biocbuild/bbs-3.9-bioc/meat/BufferedMatrix.Rcheck/tests/BMdc5f12b08785"
[13] "/Users/biocbuild/bbs-3.9-bioc/meat/BufferedMatrix.Rcheck/tests/BMdc5f3913659"
[14] "/Users/biocbuild/bbs-3.9-bioc/meat/BufferedMatrix.Rcheck/tests/BMdc5f32870ee3"
[15] "/Users/biocbuild/bbs-3.9-bioc/meat/BufferedMatrix.Rcheck/tests/BMdc5f40e272ff"
>
>
> ### 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: 0x7f8929d148f0>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x7f8929d148f0>
Warning message:
In dir.create(new.directory) :
'/Users/biocbuild/bbs-3.9-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x7f8929d148f0>
> rowMedians(tmp)
[1] -0.2272954604 -0.0209699864 0.2591483738 -0.0156227737 -0.2201796046
[6] 0.5704390068 0.0360702632 0.3449374322 0.3501636487 0.1865711851
[11] -0.1324309616 0.4670976900 -0.0553841514 0.0558004332 -0.1153765691
[16] -0.2225761142 0.3525677501 0.2231391328 0.0081789053 -0.2265267276
[21] 0.2010695332 0.3538832576 -0.0503787594 -0.3580308529 -0.5040571659
[26] 0.3483371329 0.0582982364 -0.5294569795 0.9434065900 -0.0091181862
[31] 0.2374631063 0.5594345379 -0.3464547542 -0.4670711215 0.2347619177
[36] 0.0353976780 -0.6596623622 -0.2051049475 0.2590961149 0.3180048802
[41] 0.5839759873 -0.5719084324 -0.1643534413 0.0809459007 -0.1714967076
[46] -0.0043236418 0.1814223377 0.1917636425 -0.2336320535 -0.1352564800
[51] 0.8854803107 -0.2417497172 -0.2672793269 0.0708361783 0.4564189087
[56] 0.3106912197 -0.1219592717 -0.3288548490 -0.3364181774 -0.8841531512
[61] 0.1767002290 -0.3013422862 -1.1661656187 0.0031027184 0.0906820842
[66] 0.2639599708 -0.2076907167 -0.0633854725 0.3336259700 0.1722108979
[71] 0.0461514835 0.0330758797 0.9740271341 -0.5459499401 0.8033168203
[76] 0.0079257327 0.1475415833 0.3182818266 0.0022088029 -0.0978740686
[81] -0.6351213972 0.3501004618 -0.5175277722 -0.1511071470 0.0714512752
[86] 0.4831800138 0.0915328773 -0.2383065487 -0.2546102932 -0.3476591443
[91] -0.1356068738 0.2059451175 -0.3622649477 0.2131200766 0.0424923698
[96] -0.2134456730 0.1482980087 0.0401175298 0.5324374243 -0.0785147637
[101] 0.0181130094 0.0294305996 0.0812950828 0.4730382012 0.0480358685
[106] -0.0452374223 -0.0815861390 -0.4298676751 0.2593880563 0.1042214122
[111] -0.3488490495 -0.1068180046 0.6859683764 0.3688461329 0.0316822070
[116] -0.0266465563 -0.3221068613 0.0991986813 -0.2252275785 0.0006877512
[121] -0.2748027387 0.1543223899 -0.2443169386 0.1360525402 -0.2214684435
[126] 0.5833382136 -0.6612105322 0.1535038394 -0.2409080758 -0.0624540166
[131] -0.3165146833 -0.1368650583 -0.4208189768 -0.5230141025 0.1960234974
[136] 0.6662875268 -0.4351753075 0.2054783448 0.4100336289 0.2835582661
[141] -0.2091300899 -0.2617012519 0.1102446057 -0.4253001796 -0.2264382485
[146] -0.1997549428 0.1738142374 0.1150214062 -0.1946608800 -0.2032820257
[151] -0.3685787027 -0.0141052603 -0.2905807564 -0.2819850068 -0.1866322810
[156] -0.0082285899 -0.3081379936 -0.5437281086 -0.1910748858 0.3321689292
[161] -0.0877192163 -0.5796334452 0.1432709950 0.0617356325 -0.1518167701
[166] -0.2442190078 0.0058443566 -0.1168319044 0.5979357790 0.5129748812
[171] 0.1080893050 -0.2042678494 0.1665392237 -0.2369974833 0.1100499592
[176] -0.0201895937 -0.1424450000 0.2145472255 0.1553435210 0.1613845239
[181] 0.3201613087 0.0714894853 -0.2589448016 -0.3451018624 -0.1936113959
[186] -0.0811809207 0.3357336957 0.2312253794 -0.3777129692 -0.2578369729
[191] 0.2110724662 0.5256892420 -0.0022267461 -0.1099925017 0.2014406043
[196] 0.1159114016 0.3536314180 0.3477223641 -0.0478361630 -0.5375354654
[201] 0.0337907385 -0.1023719631 0.2685743841 -0.6273583264 0.1921554882
[206] -0.2977779967 -0.0459468610 0.3958387236 0.5077615060 0.4808643685
[211] -0.0980846310 -0.3629372693 0.3902191075 0.2128584346 0.1884714817
[216] -0.2267540430 -0.1005121423 -0.3142123819 -0.0163074778 0.2696953003
[221] 0.0123496352 0.0373643783 -0.1311163097 -0.0252421346 -0.5168344877
[226] -0.1247569759 0.2319524078 0.2625262101 -0.2203191405 0.0651318269
>
> proc.time()
user system elapsed
4.106 6.885 11.303
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
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: 0x7fa5a0400250>
> .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: 0x7fa5a0400250>
> .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: 0x7fa5a0400250>
> .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: 0x7fa5a0400250>
> 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: 0x7fa5a0624320>
> .Call("R_bm_AddColumn",P)
<pointer: 0x7fa5a0624320>
> .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: 0x7fa5a0624320>
> .Call("R_bm_AddColumn",P)
<pointer: 0x7fa5a0624320>
> .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: 0x7fa5a0624320>
> 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: 0x7fa5a6d2a1f0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x7fa5a6d2a1f0>
> .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: 0x7fa5a6d2a1f0>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x7fa5a6d2a1f0>
> .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: 0x7fa5a6d2a1f0>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x7fa5a6d2a1f0>
> .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: 0x7fa5a6d2a1f0>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x7fa5a6d2a1f0>
> .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: 0x7fa5a6d2a1f0>
> 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: 0x7fa5a051faa0>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x7fa5a051faa0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x7fa5a051faa0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x7fa5a051faa0>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFilee05e565502f4" "BufferedMatrixFilee05e67350d73"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFilee05e565502f4" "BufferedMatrixFilee05e67350d73"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x7fa5aa1039c0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x7fa5aa1039c0>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x7fa5aa1039c0>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x7fa5aa1039c0>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x7fa5aa1039c0>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x7fa5aa1039c0>
> .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: 0x7fa5a6f09b40>
> .Call("R_bm_AddColumn",P)
<pointer: 0x7fa5a6f09b40>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x7fa5a6f09b40>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x7fa5a6f09b40>
> 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: 0x7fa5a6f09eb0>
> .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: 0x7fa5a6f09eb0>
> rm(P)
>
> proc.time()
user system elapsed
0.456 0.118 0.543
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
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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
0.398 0.082 0.455