| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-02-03 02:35:46 -0000 (Fri, 03 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4039 |
| 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 | ||||
|
To the developers/maintainers of the BufferedMatrix package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 228/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BufferedMatrix 1.63.0 (landing page) Ben Bolstad
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: BufferedMatrix |
| Version: 1.63.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings BufferedMatrix_1.63.0.tar.gz |
| StartedAt: 2023-02-02 02:24:28 -0000 (Thu, 02 Feb 2023) |
| EndedAt: 2023-02-02 02:25:05 -0000 (Thu, 02 Feb 2023) |
| EllapsedTime: 36.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BufferedMatrix.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings BufferedMatrix_1.63.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘BufferedMatrix/DESCRIPTION’ ... OK
* this is package ‘BufferedMatrix’ version ‘1.63.0’
* 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 11.3.0-1ubuntu1~22.04) 11.3.0’
* 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 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 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 ...
‘BufferedMatrix.Rnw’... OK
OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/00check.log’
for details.
BufferedMatrix.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL BufferedMatrix
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘BufferedMatrix’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c RBufferedMatrix.c -o RBufferedMatrix.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -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){
| ^~~~~~~~~~~~~~~~~~~
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 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c doubleBufferedMatrix_C_tests.c -o doubleBufferedMatrix_C_tests.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c init_package.c -o init_package.o
gcc -shared -L/home/biocbuild/bbs-3.17-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-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/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 Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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
0.341 0.033 0.369
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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] "/home/biocbuild/bbs-3.17-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 456993 24.5 979984 52.4 651420 34.8
Vcells 842364 6.5 8388608 64.0 2047783 15.7
>
>
>
>
> ##
> ## checking reads
> ##
>
> tmp2 <- createBufferedMatrix(10,20)
>
> test.sample <- rnorm(10*20)
>
> tmp2[1:10,1:20] <- test.sample
>
> test.matrix <- matrix(test.sample,10,20)
>
> ## testing reads
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ which.col <- sample(1:20,1)
+ if (tmp2[which.row,which.col] != test.matrix[which.row,which.col]){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> date()
[1] "Thu Feb 2 02:24:50 2023"
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
> date()
[1] "Thu Feb 2 02:24:50 2023"
>
>
> 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: 0xaaab130588e0>
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ which.col <- sample(1:20,1)
+ if (tmp2[which.row,which.col] != test.matrix[which.row,which.col]){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,5,replace=TRUE)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> date()
[1] "Thu Feb 2 02:24:50 2023"
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:20,5,replace=TRUE)
+ if (!all(tmp2[which.row,which.col] == test.matrix[which.row,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
> date()
[1] "Thu Feb 2 02:24:50 2023"
>
> ColMode(tmp2)
<pointer: 0xaaab130588e0>
>
>
>
> ### 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,] 100.48982124 -0.9481256 -0.87880741 -1.5503242
[2,] 0.09677501 0.4426524 0.05537409 -0.8208891
[3,] 0.20343168 0.1274400 0.80162269 1.0736944
[4,] 0.19789673 -1.5748440 -1.61801065 -0.8466264
> ewApply(tmp5,abs)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 2 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 100.48982124 0.9481256 0.87880741 1.5503242
[2,] 0.09677501 0.4426524 0.05537409 0.8208891
[3,] 0.20343168 0.1274400 0.80162269 1.0736944
[4,] 0.19789673 1.5748440 1.61801065 0.8466264
> ewApply(tmp5,sqrt)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.17-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,] 10.0244611 0.9737174 0.9374473 1.2451202
[2,] 0.3110868 0.6653212 0.2353170 0.9060293
[3,] 0.4510340 0.3569875 0.8953338 1.0361923
[4,] 0.4448558 1.2549279 1.2720105 0.9201230
>
> 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-3.17-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,] 225.73443 35.68530 35.25328 39.00153
[2,] 28.20764 32.09586 27.40854 34.88118
[3,] 29.71377 28.69731 34.75496 36.43562
[4,] 29.64646 39.12412 39.33812 35.04786
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0xaaab127d7470>
> exp(tmp5)
<pointer: 0xaaab127d7470>
> log(tmp5,2)
<pointer: 0xaaab127d7470>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 469.8366
> Min(tmp5)
[1] 53.5426
> mean(tmp5)
[1] 72.48239
> Sum(tmp5)
[1] 14496.48
> Var(tmp5)
[1] 866.2536
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 89.73515 70.41676 71.65324 69.79096 68.28371 71.88959 71.20496 69.94409
[9] 71.40129 70.50419
> rowSums(tmp5)
[1] 1794.703 1408.335 1433.065 1395.819 1365.674 1437.792 1424.099 1398.882
[9] 1428.026 1410.084
> rowVars(tmp5)
[1] 8081.75172 80.94908 46.32399 107.36929 56.23693 66.30966
[7] 53.56954 61.96045 84.50014 74.95552
> rowSd(tmp5)
[1] 89.898564 8.997170 6.806173 10.361915 7.499128 8.143074 7.319121
[8] 7.871496 9.192396 8.657685
> rowMax(tmp5)
[1] 469.83665 88.28352 81.02142 93.91813 83.47941 86.95300 82.23850
[8] 83.65328 85.70771 88.36011
> rowMin(tmp5)
[1] 53.88769 57.04729 57.50668 53.99549 57.96552 59.31399 56.54589 57.13180
[9] 54.96064 53.54260
>
> colMeans(tmp5)
[1] 109.50913 70.62900 69.58590 73.12644 74.27823 68.63707 70.45586
[8] 65.54573 72.43892 70.97443 71.29115 66.09558 73.08440 72.38618
[15] 69.50500 69.65405 70.07792 74.74793 70.20886 67.41610
> colSums(tmp5)
[1] 1095.0913 706.2900 695.8590 731.2644 742.7823 686.3707 704.5586
[8] 655.4573 724.3892 709.7443 712.9115 660.9558 730.8440 723.8618
[15] 695.0500 696.5405 700.7792 747.4793 702.0886 674.1610
> colVars(tmp5)
[1] 16095.32537 56.61838 96.33321 34.26415 88.40203 129.98080
[7] 43.47485 100.96985 111.69198 42.44700 28.29969 77.16909
[13] 80.10254 77.85347 80.82298 21.24567 79.86084 78.07783
[19] 19.78136 81.18884
> colSd(tmp5)
[1] 126.867353 7.524518 9.814949 5.853559 9.402236 11.400912
[7] 6.593546 10.048375 10.568443 6.515136 5.319746 8.784594
[13] 8.950002 8.823461 8.990160 4.609303 8.936490 8.836166
[19] 4.447624 9.010485
> colMax(tmp5)
[1] 469.83665 81.43174 85.01570 81.17657 88.28352 93.91813 76.98593
[8] 83.57035 88.36011 77.48780 82.23850 78.55467 85.70771 84.14562
[15] 79.85003 75.51350 81.32155 83.37776 77.40214 83.65328
> colMin(tmp5)
[1] 58.71051 57.94786 57.04729 62.69424 60.57699 53.91372 58.91030 53.88769
[9] 57.13180 58.37060 64.34194 53.99549 57.96552 59.44796 53.54260 60.07052
[17] 56.98437 59.31399 62.69923 56.54589
>
>
> ### 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] 89.73515 70.41676 71.65324 69.79096 68.28371 NA 71.20496 69.94409
[9] 71.40129 70.50419
> rowSums(tmp5)
[1] 1794.703 1408.335 1433.065 1395.819 1365.674 NA 1424.099 1398.882
[9] 1428.026 1410.084
> rowVars(tmp5)
[1] 8081.75172 80.94908 46.32399 107.36929 56.23693 68.16079
[7] 53.56954 61.96045 84.50014 74.95552
> rowSd(tmp5)
[1] 89.898564 8.997170 6.806173 10.361915 7.499128 8.255955 7.319121
[8] 7.871496 9.192396 8.657685
> rowMax(tmp5)
[1] 469.83665 88.28352 81.02142 93.91813 83.47941 NA 82.23850
[8] 83.65328 85.70771 88.36011
> rowMin(tmp5)
[1] 53.88769 57.04729 57.50668 53.99549 57.96552 NA 56.54589 57.13180
[9] 54.96064 53.54260
>
> colMeans(tmp5)
[1] 109.50913 70.62900 69.58590 73.12644 74.27823 68.63707 70.45586
[8] 65.54573 72.43892 NA 71.29115 66.09558 73.08440 72.38618
[15] 69.50500 69.65405 70.07792 74.74793 70.20886 67.41610
> colSums(tmp5)
[1] 1095.0913 706.2900 695.8590 731.2644 742.7823 686.3707 704.5586
[8] 655.4573 724.3892 NA 712.9115 660.9558 730.8440 723.8618
[15] 695.0500 696.5405 700.7792 747.4793 702.0886 674.1610
> colVars(tmp5)
[1] 16095.32537 56.61838 96.33321 34.26415 88.40203 129.98080
[7] 43.47485 100.96985 111.69198 NA 28.29969 77.16909
[13] 80.10254 77.85347 80.82298 21.24567 79.86084 78.07783
[19] 19.78136 81.18884
> colSd(tmp5)
[1] 126.867353 7.524518 9.814949 5.853559 9.402236 11.400912
[7] 6.593546 10.048375 10.568443 NA 5.319746 8.784594
[13] 8.950002 8.823461 8.990160 4.609303 8.936490 8.836166
[19] 4.447624 9.010485
> colMax(tmp5)
[1] 469.83665 81.43174 85.01570 81.17657 88.28352 93.91813 76.98593
[8] 83.57035 88.36011 NA 82.23850 78.55467 85.70771 84.14562
[15] 79.85003 75.51350 81.32155 83.37776 77.40214 83.65328
> colMin(tmp5)
[1] 58.71051 57.94786 57.04729 62.69424 60.57699 53.91372 58.91030 53.88769
[9] 57.13180 NA 64.34194 53.99549 57.96552 59.44796 53.54260 60.07052
[17] 56.98437 59.31399 62.69923 56.54589
>
> Max(tmp5,na.rm=TRUE)
[1] 469.8366
> Min(tmp5,na.rm=TRUE)
[1] 53.5426
> mean(tmp5,na.rm=TRUE)
[1] 72.45724
> Sum(tmp5,na.rm=TRUE)
[1] 14418.99
> Var(tmp5,na.rm=TRUE)
[1] 870.5014
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 89.73515 70.41676 71.65324 69.79096 68.28371 71.59495 71.20496 69.94409
[9] 71.40129 70.50419
> rowSums(tmp5,na.rm=TRUE)
[1] 1794.703 1408.335 1433.065 1395.819 1365.674 1360.304 1424.099 1398.882
[9] 1428.026 1410.084
> rowVars(tmp5,na.rm=TRUE)
[1] 8081.75172 80.94908 46.32399 107.36929 56.23693 68.16079
[7] 53.56954 61.96045 84.50014 74.95552
> rowSd(tmp5,na.rm=TRUE)
[1] 89.898564 8.997170 6.806173 10.361915 7.499128 8.255955 7.319121
[8] 7.871496 9.192396 8.657685
> rowMax(tmp5,na.rm=TRUE)
[1] 469.83665 88.28352 81.02142 93.91813 83.47941 86.95300 82.23850
[8] 83.65328 85.70771 88.36011
> rowMin(tmp5,na.rm=TRUE)
[1] 53.88769 57.04729 57.50668 53.99549 57.96552 59.31399 56.54589 57.13180
[9] 54.96064 53.54260
>
> colMeans(tmp5,na.rm=TRUE)
[1] 109.50913 70.62900 69.58590 73.12644 74.27823 68.63707 70.45586
[8] 65.54573 72.43892 70.25073 71.29115 66.09558 73.08440 72.38618
[15] 69.50500 69.65405 70.07792 74.74793 70.20886 67.41610
> colSums(tmp5,na.rm=TRUE)
[1] 1095.0913 706.2900 695.8590 731.2644 742.7823 686.3707 704.5586
[8] 655.4573 724.3892 632.2566 712.9115 660.9558 730.8440 723.8618
[15] 695.0500 696.5405 700.7792 747.4793 702.0886 674.1610
> colVars(tmp5,na.rm=TRUE)
[1] 16095.32537 56.61838 96.33321 34.26415 88.40203 129.98080
[7] 43.47485 100.96985 111.69198 41.86067 28.29969 77.16909
[13] 80.10254 77.85347 80.82298 21.24567 79.86084 78.07783
[19] 19.78136 81.18884
> colSd(tmp5,na.rm=TRUE)
[1] 126.867353 7.524518 9.814949 5.853559 9.402236 11.400912
[7] 6.593546 10.048375 10.568443 6.469982 5.319746 8.784594
[13] 8.950002 8.823461 8.990160 4.609303 8.936490 8.836166
[19] 4.447624 9.010485
> colMax(tmp5,na.rm=TRUE)
[1] 469.83665 81.43174 85.01570 81.17657 88.28352 93.91813 76.98593
[8] 83.57035 88.36011 77.23893 82.23850 78.55467 85.70771 84.14562
[15] 79.85003 75.51350 81.32155 83.37776 77.40214 83.65328
> colMin(tmp5,na.rm=TRUE)
[1] 58.71051 57.94786 57.04729 62.69424 60.57699 53.91372 58.91030 53.88769
[9] 57.13180 58.37060 64.34194 53.99549 57.96552 59.44796 53.54260 60.07052
[17] 56.98437 59.31399 62.69923 56.54589
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 89.73515 70.41676 71.65324 69.79096 68.28371 NaN 71.20496 69.94409
[9] 71.40129 70.50419
> rowSums(tmp5,na.rm=TRUE)
[1] 1794.703 1408.335 1433.065 1395.819 1365.674 0.000 1424.099 1398.882
[9] 1428.026 1410.084
> rowVars(tmp5,na.rm=TRUE)
[1] 8081.75172 80.94908 46.32399 107.36929 56.23693 NA
[7] 53.56954 61.96045 84.50014 74.95552
> rowSd(tmp5,na.rm=TRUE)
[1] 89.898564 8.997170 6.806173 10.361915 7.499128 NA 7.319121
[8] 7.871496 9.192396 8.657685
> rowMax(tmp5,na.rm=TRUE)
[1] 469.83665 88.28352 81.02142 93.91813 83.47941 NA 82.23850
[8] 83.65328 85.70771 88.36011
> rowMin(tmp5,na.rm=TRUE)
[1] 53.88769 57.04729 57.50668 53.99549 57.96552 NA 56.54589 57.13180
[9] 54.96064 53.54260
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 113.08389 70.28855 67.87147 73.87804 72.86992 68.81203 70.14045
[8] 63.54300 73.16355 NaN 71.95609 65.90240 72.72875 73.18319
[15] 68.35555 69.45804 69.77295 76.46281 70.95885 68.28496
> colSums(tmp5,na.rm=TRUE)
[1] 1017.7550 632.5969 610.8433 664.9024 655.8293 619.3083 631.2641
[8] 571.8870 658.4720 0.0000 647.6048 593.1216 654.5587 658.6487
[15] 615.1999 625.1223 627.9565 688.1653 638.6296 614.5647
> colVars(tmp5,na.rm=TRUE)
[1] 17963.47827 62.39170 75.30835 32.19202 77.13982 145.88400
[7] 47.79006 68.46789 119.74624 NA 26.86301 86.39538
[13] 88.69234 80.43878 76.06199 23.46916 88.79710 54.75334
[19] 15.92618 82.84460
> colSd(tmp5,na.rm=TRUE)
[1] 134.027901 7.898842 8.678038 5.673801 8.782928 12.078245
[7] 6.913036 8.274533 10.942863 NA 5.182954 9.294911
[13] 9.417661 8.968767 8.721353 4.844497 9.423222 7.399550
[19] 3.990761 9.101901
> colMax(tmp5,na.rm=TRUE)
[1] 469.83665 81.43174 81.87713 81.17657 88.28352 93.91813 76.98593
[8] 80.82173 88.36011 -Inf 82.23850 78.55467 85.70771 84.14562
[15] 79.71547 75.51350 81.32155 83.37776 77.40214 83.65328
> colMin(tmp5,na.rm=TRUE)
[1] 58.71051 57.94786 57.04729 62.69424 60.57699 53.91372 58.91030 53.88769
[9] 57.13180 Inf 64.34194 53.99549 57.96552 59.44796 53.54260 60.07052
[17] 56.98437 62.84419 62.69923 56.54589
>
>
>
>
> 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] 154.2059 110.7498 208.3980 256.8380 235.7269 229.7765 206.6852 162.1313
[9] 234.7401 104.3516
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 154.2059 110.7498 208.3980 256.8380 235.7269 229.7765 206.6852 162.1313
[9] 234.7401 104.3516
>
>
>
> 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] 0.000000e+00 1.136868e-13 -5.684342e-14 -5.684342e-14 2.842171e-14
[6] 2.842171e-14 2.842171e-14 -1.136868e-13 -1.705303e-13 5.684342e-14
[11] 8.526513e-14 0.000000e+00 -2.842171e-14 -5.684342e-14 -2.273737e-13
[16] 5.684342e-14 0.000000e+00 2.273737e-13 -5.684342e-14 0.000000e+00
>
>
>
>
>
>
>
>
>
>
> ## 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)
+ }
7 8
8 12
8 1
2 9
1 4
1 1
9 3
10 19
2 2
5 8
5 1
5 2
1 19
4 10
10 11
1 15
9 15
4 18
9 14
8 11
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] 3.303402
> Min(tmp)
[1] -2.148354
> mean(tmp)
[1] 0.1606672
> Sum(tmp)
[1] 16.06672
> Var(tmp)
[1] 0.9196447
>
> rowMeans(tmp)
[1] 0.1606672
> rowSums(tmp)
[1] 16.06672
> rowVars(tmp)
[1] 0.9196447
> rowSd(tmp)
[1] 0.9589811
> rowMax(tmp)
[1] 3.303402
> rowMin(tmp)
[1] -2.148354
>
> colMeans(tmp)
[1] -0.096088439 -0.258219318 0.948193342 0.193085631 0.748235027
[6] 1.083372633 0.219649407 2.383560110 -0.439661831 -0.575924498
[11] 2.804416022 -0.938527440 0.547416415 0.166960738 -1.754541695
[16] 0.008161252 0.700078364 1.184621964 0.840212422 0.436649868
[21] -0.576323740 -0.251947258 0.287938010 0.554852568 0.211598585
[26] 0.053511303 0.077541216 0.545564397 -1.572341889 -0.640050922
[31] 0.960689884 -0.650091297 0.764218031 -0.398211000 0.024657001
[36] -1.569541947 0.693586347 -0.102203001 0.430268520 0.718167029
[41] -0.435881156 -2.148353812 -0.102922279 -0.942529947 0.405981120
[46] -0.010944962 -1.065449395 0.905307148 0.965703986 0.081636278
[51] 0.140237337 -1.618489132 -0.509562944 -0.236050158 -0.036083750
[56] -0.734226113 -0.261301257 1.454091013 0.553519877 0.519164745
[61] 0.432084658 -0.133272686 0.040075481 0.787043258 1.187091507
[66] 0.746360703 1.065179420 -0.259991409 0.410231098 0.829130760
[71] -0.646681507 -0.078451176 0.625105549 -2.027880285 0.832254047
[76] 1.418974817 -0.564309637 -1.295583207 -0.667884677 1.103500149
[81] 0.898043510 0.246216384 -0.321371563 -1.413518767 1.771675176
[86] 0.872496075 0.964360244 1.138771425 1.418440592 0.973025041
[91] 0.049635395 0.386752582 0.089984411 0.406137196 -1.050189763
[96] 3.303401508 -0.732763264 -1.902729656 0.454666124 0.023333018
> colSums(tmp)
[1] -0.096088439 -0.258219318 0.948193342 0.193085631 0.748235027
[6] 1.083372633 0.219649407 2.383560110 -0.439661831 -0.575924498
[11] 2.804416022 -0.938527440 0.547416415 0.166960738 -1.754541695
[16] 0.008161252 0.700078364 1.184621964 0.840212422 0.436649868
[21] -0.576323740 -0.251947258 0.287938010 0.554852568 0.211598585
[26] 0.053511303 0.077541216 0.545564397 -1.572341889 -0.640050922
[31] 0.960689884 -0.650091297 0.764218031 -0.398211000 0.024657001
[36] -1.569541947 0.693586347 -0.102203001 0.430268520 0.718167029
[41] -0.435881156 -2.148353812 -0.102922279 -0.942529947 0.405981120
[46] -0.010944962 -1.065449395 0.905307148 0.965703986 0.081636278
[51] 0.140237337 -1.618489132 -0.509562944 -0.236050158 -0.036083750
[56] -0.734226113 -0.261301257 1.454091013 0.553519877 0.519164745
[61] 0.432084658 -0.133272686 0.040075481 0.787043258 1.187091507
[66] 0.746360703 1.065179420 -0.259991409 0.410231098 0.829130760
[71] -0.646681507 -0.078451176 0.625105549 -2.027880285 0.832254047
[76] 1.418974817 -0.564309637 -1.295583207 -0.667884677 1.103500149
[81] 0.898043510 0.246216384 -0.321371563 -1.413518767 1.771675176
[86] 0.872496075 0.964360244 1.138771425 1.418440592 0.973025041
[91] 0.049635395 0.386752582 0.089984411 0.406137196 -1.050189763
[96] 3.303401508 -0.732763264 -1.902729656 0.454666124 0.023333018
> 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] -0.096088439 -0.258219318 0.948193342 0.193085631 0.748235027
[6] 1.083372633 0.219649407 2.383560110 -0.439661831 -0.575924498
[11] 2.804416022 -0.938527440 0.547416415 0.166960738 -1.754541695
[16] 0.008161252 0.700078364 1.184621964 0.840212422 0.436649868
[21] -0.576323740 -0.251947258 0.287938010 0.554852568 0.211598585
[26] 0.053511303 0.077541216 0.545564397 -1.572341889 -0.640050922
[31] 0.960689884 -0.650091297 0.764218031 -0.398211000 0.024657001
[36] -1.569541947 0.693586347 -0.102203001 0.430268520 0.718167029
[41] -0.435881156 -2.148353812 -0.102922279 -0.942529947 0.405981120
[46] -0.010944962 -1.065449395 0.905307148 0.965703986 0.081636278
[51] 0.140237337 -1.618489132 -0.509562944 -0.236050158 -0.036083750
[56] -0.734226113 -0.261301257 1.454091013 0.553519877 0.519164745
[61] 0.432084658 -0.133272686 0.040075481 0.787043258 1.187091507
[66] 0.746360703 1.065179420 -0.259991409 0.410231098 0.829130760
[71] -0.646681507 -0.078451176 0.625105549 -2.027880285 0.832254047
[76] 1.418974817 -0.564309637 -1.295583207 -0.667884677 1.103500149
[81] 0.898043510 0.246216384 -0.321371563 -1.413518767 1.771675176
[86] 0.872496075 0.964360244 1.138771425 1.418440592 0.973025041
[91] 0.049635395 0.386752582 0.089984411 0.406137196 -1.050189763
[96] 3.303401508 -0.732763264 -1.902729656 0.454666124 0.023333018
> colMin(tmp)
[1] -0.096088439 -0.258219318 0.948193342 0.193085631 0.748235027
[6] 1.083372633 0.219649407 2.383560110 -0.439661831 -0.575924498
[11] 2.804416022 -0.938527440 0.547416415 0.166960738 -1.754541695
[16] 0.008161252 0.700078364 1.184621964 0.840212422 0.436649868
[21] -0.576323740 -0.251947258 0.287938010 0.554852568 0.211598585
[26] 0.053511303 0.077541216 0.545564397 -1.572341889 -0.640050922
[31] 0.960689884 -0.650091297 0.764218031 -0.398211000 0.024657001
[36] -1.569541947 0.693586347 -0.102203001 0.430268520 0.718167029
[41] -0.435881156 -2.148353812 -0.102922279 -0.942529947 0.405981120
[46] -0.010944962 -1.065449395 0.905307148 0.965703986 0.081636278
[51] 0.140237337 -1.618489132 -0.509562944 -0.236050158 -0.036083750
[56] -0.734226113 -0.261301257 1.454091013 0.553519877 0.519164745
[61] 0.432084658 -0.133272686 0.040075481 0.787043258 1.187091507
[66] 0.746360703 1.065179420 -0.259991409 0.410231098 0.829130760
[71] -0.646681507 -0.078451176 0.625105549 -2.027880285 0.832254047
[76] 1.418974817 -0.564309637 -1.295583207 -0.667884677 1.103500149
[81] 0.898043510 0.246216384 -0.321371563 -1.413518767 1.771675176
[86] 0.872496075 0.964360244 1.138771425 1.418440592 0.973025041
[91] 0.049635395 0.386752582 0.089984411 0.406137196 -1.050189763
[96] 3.303401508 -0.732763264 -1.902729656 0.454666124 0.023333018
> colMedians(tmp)
[1] -0.096088439 -0.258219318 0.948193342 0.193085631 0.748235027
[6] 1.083372633 0.219649407 2.383560110 -0.439661831 -0.575924498
[11] 2.804416022 -0.938527440 0.547416415 0.166960738 -1.754541695
[16] 0.008161252 0.700078364 1.184621964 0.840212422 0.436649868
[21] -0.576323740 -0.251947258 0.287938010 0.554852568 0.211598585
[26] 0.053511303 0.077541216 0.545564397 -1.572341889 -0.640050922
[31] 0.960689884 -0.650091297 0.764218031 -0.398211000 0.024657001
[36] -1.569541947 0.693586347 -0.102203001 0.430268520 0.718167029
[41] -0.435881156 -2.148353812 -0.102922279 -0.942529947 0.405981120
[46] -0.010944962 -1.065449395 0.905307148 0.965703986 0.081636278
[51] 0.140237337 -1.618489132 -0.509562944 -0.236050158 -0.036083750
[56] -0.734226113 -0.261301257 1.454091013 0.553519877 0.519164745
[61] 0.432084658 -0.133272686 0.040075481 0.787043258 1.187091507
[66] 0.746360703 1.065179420 -0.259991409 0.410231098 0.829130760
[71] -0.646681507 -0.078451176 0.625105549 -2.027880285 0.832254047
[76] 1.418974817 -0.564309637 -1.295583207 -0.667884677 1.103500149
[81] 0.898043510 0.246216384 -0.321371563 -1.413518767 1.771675176
[86] 0.872496075 0.964360244 1.138771425 1.418440592 0.973025041
[91] 0.049635395 0.386752582 0.089984411 0.406137196 -1.050189763
[96] 3.303401508 -0.732763264 -1.902729656 0.454666124 0.023333018
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] -0.09608844 -0.2582193 0.9481933 0.1930856 0.748235 1.083373 0.2196494
[2,] -0.09608844 -0.2582193 0.9481933 0.1930856 0.748235 1.083373 0.2196494
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] 2.38356 -0.4396618 -0.5759245 2.804416 -0.9385274 0.5474164 0.1669607
[2,] 2.38356 -0.4396618 -0.5759245 2.804416 -0.9385274 0.5474164 0.1669607
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] -1.754542 0.008161252 0.7000784 1.184622 0.8402124 0.4366499 -0.5763237
[2,] -1.754542 0.008161252 0.7000784 1.184622 0.8402124 0.4366499 -0.5763237
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] -0.2519473 0.287938 0.5548526 0.2115986 0.0535113 0.07754122 0.5455644
[2,] -0.2519473 0.287938 0.5548526 0.2115986 0.0535113 0.07754122 0.5455644
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] -1.572342 -0.6400509 0.9606899 -0.6500913 0.764218 -0.398211 0.024657
[2,] -1.572342 -0.6400509 0.9606899 -0.6500913 0.764218 -0.398211 0.024657
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] -1.569542 0.6935863 -0.102203 0.4302685 0.718167 -0.4358812 -2.148354
[2,] -1.569542 0.6935863 -0.102203 0.4302685 0.718167 -0.4358812 -2.148354
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] -0.1029223 -0.9425299 0.4059811 -0.01094496 -1.065449 0.9053071 0.965704
[2,] -0.1029223 -0.9425299 0.4059811 -0.01094496 -1.065449 0.9053071 0.965704
[,50] [,51] [,52] [,53] [,54] [,55]
[1,] 0.08163628 0.1402373 -1.618489 -0.5095629 -0.2360502 -0.03608375
[2,] 0.08163628 0.1402373 -1.618489 -0.5095629 -0.2360502 -0.03608375
[,56] [,57] [,58] [,59] [,60] [,61] [,62]
[1,] -0.7342261 -0.2613013 1.454091 0.5535199 0.5191647 0.4320847 -0.1332727
[2,] -0.7342261 -0.2613013 1.454091 0.5535199 0.5191647 0.4320847 -0.1332727
[,63] [,64] [,65] [,66] [,67] [,68] [,69]
[1,] 0.04007548 0.7870433 1.187092 0.7463607 1.065179 -0.2599914 0.4102311
[2,] 0.04007548 0.7870433 1.187092 0.7463607 1.065179 -0.2599914 0.4102311
[,70] [,71] [,72] [,73] [,74] [,75] [,76]
[1,] 0.8291308 -0.6466815 -0.07845118 0.6251055 -2.02788 0.832254 1.418975
[2,] 0.8291308 -0.6466815 -0.07845118 0.6251055 -2.02788 0.832254 1.418975
[,77] [,78] [,79] [,80] [,81] [,82] [,83]
[1,] -0.5643096 -1.295583 -0.6678847 1.1035 0.8980435 0.2462164 -0.3213716
[2,] -0.5643096 -1.295583 -0.6678847 1.1035 0.8980435 0.2462164 -0.3213716
[,84] [,85] [,86] [,87] [,88] [,89] [,90]
[1,] -1.413519 1.771675 0.8724961 0.9643602 1.138771 1.418441 0.973025
[2,] -1.413519 1.771675 0.8724961 0.9643602 1.138771 1.418441 0.973025
[,91] [,92] [,93] [,94] [,95] [,96] [,97]
[1,] 0.04963539 0.3867526 0.08998441 0.4061372 -1.05019 3.303402 -0.7327633
[2,] 0.04963539 0.3867526 0.08998441 0.4061372 -1.05019 3.303402 -0.7327633
[,98] [,99] [,100]
[1,] -1.90273 0.4546661 0.02333302
[2,] -1.90273 0.4546661 0.02333302
>
>
> Max(tmp2)
[1] 2.722079
> Min(tmp2)
[1] -2.799543
> mean(tmp2)
[1] 0.06975382
> Sum(tmp2)
[1] 6.975382
> Var(tmp2)
[1] 1.000402
>
> rowMeans(tmp2)
[1] 1.44674351 0.61547087 -1.31579498 -2.18149494 0.37346718 -0.18850927
[7] 1.29015891 0.28085589 1.03496872 2.57856877 -0.11882046 -0.80851689
[13] -0.20738473 0.97960515 0.65735997 0.29770551 -0.27091687 -0.37997240
[19] 0.24278337 -0.08439089 2.13739713 0.28421115 0.57107104 0.40251885
[25] -0.12838875 -1.25233574 0.48808449 0.34724386 1.26227528 0.17847597
[31] -0.39158770 -0.88224001 -0.46718949 0.53157474 -0.89262882 1.18848387
[37] -0.14250015 0.13667188 1.00166577 -0.29915662 -1.31717608 0.47148239
[43] -0.70393525 0.83816975 -0.31747376 0.77323997 0.42432073 1.83442781
[49] 0.20855365 1.47763369 -0.40068113 2.72207905 -0.04073581 0.15442503
[55] 0.79686561 0.01671564 -0.07940422 0.80897382 -0.24248719 -2.19299933
[61] 0.96040892 0.21042868 0.01143674 0.68149215 -0.60074771 0.51013647
[67] -1.52579379 0.85551146 -0.03445056 -0.88485895 -0.42818341 -0.37326726
[73] -1.58565721 0.07753456 -0.94425544 -0.27347266 -0.30699964 0.24580370
[79] 0.40354643 1.14740945 1.34176091 -0.44731508 -0.80740274 0.44600685
[85] -2.02187467 -0.58241997 -0.61461095 0.37812340 0.29124578 0.05230961
[91] 2.11861602 0.74409170 -2.79954278 0.95020846 -1.74614442 -1.37138058
[97] -1.11572597 1.37701951 -0.24357769 -0.66755451
> rowSums(tmp2)
[1] 1.44674351 0.61547087 -1.31579498 -2.18149494 0.37346718 -0.18850927
[7] 1.29015891 0.28085589 1.03496872 2.57856877 -0.11882046 -0.80851689
[13] -0.20738473 0.97960515 0.65735997 0.29770551 -0.27091687 -0.37997240
[19] 0.24278337 -0.08439089 2.13739713 0.28421115 0.57107104 0.40251885
[25] -0.12838875 -1.25233574 0.48808449 0.34724386 1.26227528 0.17847597
[31] -0.39158770 -0.88224001 -0.46718949 0.53157474 -0.89262882 1.18848387
[37] -0.14250015 0.13667188 1.00166577 -0.29915662 -1.31717608 0.47148239
[43] -0.70393525 0.83816975 -0.31747376 0.77323997 0.42432073 1.83442781
[49] 0.20855365 1.47763369 -0.40068113 2.72207905 -0.04073581 0.15442503
[55] 0.79686561 0.01671564 -0.07940422 0.80897382 -0.24248719 -2.19299933
[61] 0.96040892 0.21042868 0.01143674 0.68149215 -0.60074771 0.51013647
[67] -1.52579379 0.85551146 -0.03445056 -0.88485895 -0.42818341 -0.37326726
[73] -1.58565721 0.07753456 -0.94425544 -0.27347266 -0.30699964 0.24580370
[79] 0.40354643 1.14740945 1.34176091 -0.44731508 -0.80740274 0.44600685
[85] -2.02187467 -0.58241997 -0.61461095 0.37812340 0.29124578 0.05230961
[91] 2.11861602 0.74409170 -2.79954278 0.95020846 -1.74614442 -1.37138058
[97] -1.11572597 1.37701951 -0.24357769 -0.66755451
> 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] 1.44674351 0.61547087 -1.31579498 -2.18149494 0.37346718 -0.18850927
[7] 1.29015891 0.28085589 1.03496872 2.57856877 -0.11882046 -0.80851689
[13] -0.20738473 0.97960515 0.65735997 0.29770551 -0.27091687 -0.37997240
[19] 0.24278337 -0.08439089 2.13739713 0.28421115 0.57107104 0.40251885
[25] -0.12838875 -1.25233574 0.48808449 0.34724386 1.26227528 0.17847597
[31] -0.39158770 -0.88224001 -0.46718949 0.53157474 -0.89262882 1.18848387
[37] -0.14250015 0.13667188 1.00166577 -0.29915662 -1.31717608 0.47148239
[43] -0.70393525 0.83816975 -0.31747376 0.77323997 0.42432073 1.83442781
[49] 0.20855365 1.47763369 -0.40068113 2.72207905 -0.04073581 0.15442503
[55] 0.79686561 0.01671564 -0.07940422 0.80897382 -0.24248719 -2.19299933
[61] 0.96040892 0.21042868 0.01143674 0.68149215 -0.60074771 0.51013647
[67] -1.52579379 0.85551146 -0.03445056 -0.88485895 -0.42818341 -0.37326726
[73] -1.58565721 0.07753456 -0.94425544 -0.27347266 -0.30699964 0.24580370
[79] 0.40354643 1.14740945 1.34176091 -0.44731508 -0.80740274 0.44600685
[85] -2.02187467 -0.58241997 -0.61461095 0.37812340 0.29124578 0.05230961
[91] 2.11861602 0.74409170 -2.79954278 0.95020846 -1.74614442 -1.37138058
[97] -1.11572597 1.37701951 -0.24357769 -0.66755451
> rowMin(tmp2)
[1] 1.44674351 0.61547087 -1.31579498 -2.18149494 0.37346718 -0.18850927
[7] 1.29015891 0.28085589 1.03496872 2.57856877 -0.11882046 -0.80851689
[13] -0.20738473 0.97960515 0.65735997 0.29770551 -0.27091687 -0.37997240
[19] 0.24278337 -0.08439089 2.13739713 0.28421115 0.57107104 0.40251885
[25] -0.12838875 -1.25233574 0.48808449 0.34724386 1.26227528 0.17847597
[31] -0.39158770 -0.88224001 -0.46718949 0.53157474 -0.89262882 1.18848387
[37] -0.14250015 0.13667188 1.00166577 -0.29915662 -1.31717608 0.47148239
[43] -0.70393525 0.83816975 -0.31747376 0.77323997 0.42432073 1.83442781
[49] 0.20855365 1.47763369 -0.40068113 2.72207905 -0.04073581 0.15442503
[55] 0.79686561 0.01671564 -0.07940422 0.80897382 -0.24248719 -2.19299933
[61] 0.96040892 0.21042868 0.01143674 0.68149215 -0.60074771 0.51013647
[67] -1.52579379 0.85551146 -0.03445056 -0.88485895 -0.42818341 -0.37326726
[73] -1.58565721 0.07753456 -0.94425544 -0.27347266 -0.30699964 0.24580370
[79] 0.40354643 1.14740945 1.34176091 -0.44731508 -0.80740274 0.44600685
[85] -2.02187467 -0.58241997 -0.61461095 0.37812340 0.29124578 0.05230961
[91] 2.11861602 0.74409170 -2.79954278 0.95020846 -1.74614442 -1.37138058
[97] -1.11572597 1.37701951 -0.24357769 -0.66755451
>
> colMeans(tmp2)
[1] 0.06975382
> colSums(tmp2)
[1] 6.975382
> colVars(tmp2)
[1] 1.000402
> colSd(tmp2)
[1] 1.000201
> colMax(tmp2)
[1] 2.722079
> colMin(tmp2)
[1] -2.799543
> colMedians(tmp2)
[1] 0.1071032
> colRanges(tmp2)
[,1]
[1,] -2.799543
[2,] 2.722079
>
> dataset1 <- matrix(dataset1,1,100)
>
> agree.checks(tmp,dataset1)
>
> dataset2 <- matrix(dataset2,100,1)
> agree.checks(tmp2,dataset2)
>
>
> tmp <- createBufferedMatrix(10,10)
>
> tmp[1:10,1:10] <- rnorm(100)
> colApply(tmp,sum)
[1] -1.40077549 -0.05529549 -2.04566269 4.15968016 -2.60840118 -3.64162340
[7] 6.01319579 -1.25618032 -0.39766777 6.44220721
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.4172621
[2,] -0.6328079
[3,] -0.2147219
[4,] 0.4903236
[5,] 1.1751229
>
> rowApply(tmp,sum)
[1] 3.0532917 2.7184579 -0.7346749 3.7133817 -1.6076699 0.3589069
[7] -1.9763859 -2.0820914 0.1819132 1.5843474
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 9 1 9 4 3 8 6 5 8
[2,] 10 1 4 1 6 6 6 5 4 5
[3,] 5 7 2 7 9 8 2 4 1 3
[4,] 3 10 9 5 3 5 10 7 6 10
[5,] 2 8 6 4 8 1 7 1 8 4
[6,] 9 2 3 8 1 2 5 2 2 7
[7,] 8 5 5 10 5 7 3 10 9 6
[8,] 4 6 10 6 2 4 4 9 7 1
[9,] 6 3 7 3 7 10 1 3 3 9
[10,] 7 4 8 2 10 9 9 8 10 2
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] 2.0681167 1.5576141 1.5780364 0.1813124 -3.8324844 -2.2025399
[7] 0.6194762 -1.5973425 0.9111506 -1.5071814 3.7494479 -2.5172530
[13] 0.7727297 -1.6800106 5.6819932 -4.0871176 2.9236335 0.3431323
[19] 1.3165322 1.4966884
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.0509548
[2,] -0.2343922
[3,] 0.2661463
[4,] 1.3489072
[5,] 1.7384102
>
> rowApply(tmp,sum)
[1] 3.378330 -5.603175 5.107154 5.116646 -2.223021
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 1 20 7 12 20
[2,] 4 16 12 16 13
[3,] 20 2 11 15 19
[4,] 16 12 6 10 6
[5,] 11 6 1 2 3
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] -1.0509548 -0.8809315 2.0511096 0.9906028 0.4737779 -1.0072235
[2,] 1.7384102 1.0602695 -2.2746363 0.1188237 -1.3420897 -1.3348556
[3,] -0.2343922 0.2813984 0.2076084 -0.2940132 -1.0228168 -0.2181706
[4,] 0.2661463 0.8261358 0.6068081 0.1499874 -0.8399068 0.2312757
[5,] 1.3489072 0.2707418 0.9871465 -0.7840883 -1.1014489 0.1264341
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] 1.2429524 -0.3339980 1.7181981 0.9883469 0.90788658 -0.8103503
[2,] -2.4263625 0.7289964 -1.5560798 -1.4962314 -0.04741285 1.1438214
[3,] 0.8774346 -0.8586761 1.1904012 -0.5806189 0.40134483 -0.8680987
[4,] 1.8494772 -1.8567889 0.1027379 -0.1472727 1.53398922 -0.4075836
[5,] -0.9240255 0.7231241 -0.5441067 -0.2714054 0.95364016 -1.5750419
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] -0.4074187 -0.6417617 1.1417982 -0.4706503 0.7296424 -0.7393765
[2,] 0.3594734 -1.6731950 -0.3969459 -1.0829655 1.4870388 -0.7755333
[3,] 1.0038803 0.1257918 1.3784259 -0.8394904 1.8650149 0.1557127
[4,] -0.8182957 0.4757523 2.7661927 -0.4603660 -0.5907839 1.2552061
[5,] 0.6350904 0.0334020 0.7925223 -1.2336453 -0.5672786 0.4471234
[,19] [,20]
[1,] -1.0440509 0.5207316
[2,] 1.6711186 0.4951808
[3,] 1.7094791 0.8269389
[4,] -0.1804778 0.3544128
[5,] -0.8395368 -0.7005756
>
>
> is.BufferedMatrix(tmp)
[1] TRUE
>
> as.BufferedMatrix(as.matrix(tmp))
BufferedMatrix object
Matrix size: 5 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.17-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-3.17-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-3.17-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-3.17-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 480 bytes.
>
>
> rm(tmp)
>
>
> ###
> ### Testing colnames and rownames
> ###
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
>
>
> colnames(tmp)
NULL
> rownames(tmp)
NULL
>
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
> colnames(tmp)
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
> rownames(tmp)
[1] "row1" "row2" "row3" "row4" "row5"
>
>
> tmp["row1",]
col1 col2 col3 col4 col5 col6 col7
row1 0.4437929 -0.8340471 0.5958414 0.3740161 -0.4568191 -0.7308775 0.4667878
col8 col9 col10 col11 col12 col13 col14
row1 0.757698 1.720713 2.051298 1.009776 0.9305928 -0.2797425 -0.379648
col15 col16 col17 col18 col19 col20
row1 0.4212565 0.4867513 0.4538444 -0.5153636 -0.3945025 0.5326001
> tmp[,"col10"]
col10
row1 2.0512984
row2 -1.0917480
row3 1.4111805
row4 -1.0221717
row5 0.4600589
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7
row1 0.4437929 -0.8340471 0.5958414 0.3740161 -0.4568191 -0.7308775 0.4667878
row5 1.9420941 -0.2552995 0.6705747 0.8435052 -0.3920597 0.1918230 -0.5606784
col8 col9 col10 col11 col12 col13 col14
row1 0.7576980 1.720713 2.0512984 1.0097755 0.9305928 -0.2797425 -0.379648
row5 0.6664518 -1.190399 0.4600589 0.6062304 0.1312131 -0.4942035 1.399886
col15 col16 col17 col18 col19 col20
row1 0.4212565 0.4867513 0.45384440 -0.5153636 -0.3945025 0.5326001
row5 0.7019209 -0.8222023 0.03092268 0.0385864 0.2966650 -0.5953723
> tmp[,c("col6","col20")]
col6 col20
row1 -0.7308775 0.5326001
row2 -0.5300161 0.7956802
row3 0.2668117 1.5056638
row4 2.6815878 -1.7322914
row5 0.1918230 -0.5953723
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 -0.7308775 0.5326001
row5 0.1918230 -0.5953723
>
>
>
>
> tmp["row1",] <- rnorm(20,mean=10)
> tmp[,"col10"] <- rnorm(5,mean=30)
> tmp[c("row1","row5"),] <- rnorm(40,mean=50)
> tmp[,c("col6","col20")] <- rnorm(10,mean=75)
> tmp[c("row1","row5"),c("col6","col20")] <- rnorm(4,mean=105)
>
> tmp["row1",]
col1 col2 col3 col4 col5 col6 col7 col8
row1 51.09574 52.22086 49.09766 49.08469 50.91507 104.9764 50.24491 50.80287
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.48232 49.52953 50.61235 51.2512 51.05402 51.27168 49.3223 50.71375
col17 col18 col19 col20
row1 49.7826 49.37506 51.64814 104.8421
> tmp[,"col10"]
col10
row1 49.52953
row2 29.81190
row3 29.58689
row4 29.28479
row5 48.90526
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 51.09574 52.22086 49.09766 49.08469 50.91507 104.9764 50.24491 50.80287
row5 49.03801 51.72469 48.65030 50.85505 51.51640 103.4253 48.88574 49.79789
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.48232 49.52953 50.61235 51.25120 51.05402 51.27168 49.32230 50.71375
row5 49.47361 48.90526 49.20920 50.12873 50.25266 49.31511 51.00629 50.54654
col17 col18 col19 col20
row1 49.78260 49.37506 51.64814 104.8421
row5 50.36347 49.65906 49.47874 104.9624
> tmp[,c("col6","col20")]
col6 col20
row1 104.97637 104.84208
row2 74.59626 73.84524
row3 75.00682 74.86390
row4 75.08817 74.89169
row5 103.42532 104.96237
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 104.9764 104.8421
row5 103.4253 104.9624
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 104.9764 104.8421
row5 103.4253 104.9624
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] 0.1480941
[2,] 0.6381194
[3,] 0.2463156
[4,] -0.6646814
[5,] -1.2585490
> tmp[,c("col17","col7")]
col17 col7
[1,] 0.97983539 0.6436529
[2,] 0.27593571 -0.1406612
[3,] 0.89061853 0.6808509
[4,] 0.91614224 0.9645699
[5,] 0.03696265 -2.3633961
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] -0.5071928 -0.2781491
[2,] 0.2649331 1.2094800
[3,] 0.2189485 1.0570730
[4,] 0.6059141 0.8826225
[5,] 0.2693101 0.1306216
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] -0.5071928
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] -0.5071928
[2,] 0.2649331
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
>
>
>
> subBufferedMatrix(tmp,c("row3","row1"),)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row3 0.1302745 0.1699276 -1.773520 0.9318378 -1.074212 0.1219143 1.742736
row1 0.9325205 -0.1415611 0.313371 -1.1662830 -0.635337 1.0212240 1.162130
[,8] [,9] [,10] [,11] [,12] [,13]
row3 -1.3407435 1.2009206 0.7902544 -0.9620719 -0.5791511 -1.111983
row1 -0.6212547 -0.5511315 -0.5797292 -0.9895808 -1.3679212 -0.662089
[,14] [,15] [,16] [,17] [,18] [,19]
row3 1.5245211 -0.4211358 -0.1206397 -1.4394631 -1.0923490 -0.9533489
row1 -0.7811538 -0.8270427 0.3501125 0.5935838 0.7878519 0.6642354
[,20]
row3 0.7578958
row1 -0.5526470
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 -1.58354 -1.587302 0.8006169 1.129481 -0.7940539 -1.737913 -0.3463141
[,8] [,9] [,10]
row2 2.178973 0.2374325 -0.2306959
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 1.293809 -0.3783127 1.172188 2.887342 1.349425 1.301183 0.8936575
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 0.0696215 0.04403638 0.64251 -0.147032 -2.102639 -0.1033945 -0.9236455
[,15] [,16] [,17] [,18] [,19] [,20]
row5 -0.2589433 0.03546622 -0.786568 -0.02933756 -0.1461366 -2.015892
>
>
> 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: 0xaaab13ad9c80>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/tests/BM251fb8280d1b43"
[2] "/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/tests/BM251fb82f9a9fb2"
[3] "/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/tests/BM251fb832ca3478"
[4] "/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/tests/BM251fb840f3ea60"
[5] "/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/tests/BM251fb8125a1b4d"
[6] "/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/tests/BM251fb84a0c3189"
[7] "/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/tests/BM251fb83c2b30e4"
[8] "/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/tests/BM251fb8694bf8b6"
[9] "/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/tests/BM251fb85b4507a1"
[10] "/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/tests/BM251fb896c5397"
[11] "/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/tests/BM251fb8e56979"
[12] "/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/tests/BM251fb81a01027a"
[13] "/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/tests/BM251fb87eba323d"
[14] "/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/tests/BM251fb878ed52f8"
[15] "/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/tests/BM251fb820d27a09"
>
>
> ### 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: 0xaaab162b9d20>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0xaaab162b9d20>
Warning message:
In dir.create(new.directory) :
'/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0xaaab162b9d20>
> rowMedians(tmp)
[1] 0.0718431911 0.4146201657 -0.1973573957 0.5270464541 0.1533624990
[6] 0.2901448374 -0.1053942694 -0.6897111761 0.2848160398 0.6490782621
[11] 0.1699697657 0.2001156599 -0.4034783384 -0.4511559173 0.0937670137
[16] -0.0441462183 -0.6109237587 0.0472666849 -0.0223396924 0.0864030258
[21] 0.1130143627 -0.3178546357 0.5364237387 -0.0816845193 0.1914965321
[26] -0.4379076084 -0.0380702501 0.3736706270 0.1150819981 0.0322557075
[31] 0.5684962886 -0.0506969226 0.3997668803 0.2230197076 -0.2788415549
[36] 0.4072721300 -0.5243644813 0.1074256797 -0.5208746135 0.3480830597
[41] 0.0945532250 -0.2183885531 -0.1654286903 -0.2434560119 0.0266417022
[46] -0.3282669555 0.3155813073 -0.3278897428 0.1293264736 -0.2810486182
[51] 0.0080108824 -0.3748159415 -0.2215981545 -0.0497789384 0.6884578751
[56] 0.3778850997 -0.2197906749 -0.2413464228 0.0685901649 -0.3290981364
[61] 0.2844866100 0.3015972747 -0.0917324022 -0.1291448868 0.4257973868
[66] -0.5230901730 -0.0522490888 -0.2357222073 -0.3248397350 -0.0694078735
[71] 0.0840222791 0.0464233733 -0.0113047154 0.3176533737 -0.4428465692
[76] -0.7343126564 0.2858731715 0.0745044991 -0.3009289765 -0.3335133339
[81] -0.3631833778 0.1096928955 -0.2893464508 -0.1943524937 -0.0657103754
[86] -0.1313096179 0.5052531588 0.0738724125 -0.2619298978 -0.2857835215
[91] 0.1624403087 0.1296154328 -0.0232248714 -0.3423780049 -0.2143433449
[96] 0.2202491259 -0.1541722382 0.0683209295 0.2988791495 -0.5351427452
[101] -0.4042334355 0.3411694027 -0.2226365537 -0.1600932294 -0.1734703462
[106] 0.0302828149 0.3168812760 0.0291122963 0.2964495907 0.0845025138
[111] 0.2482108411 0.3883335066 0.3026730928 0.5437188449 -0.1971041680
[116] 0.0467560830 0.0438055607 -0.3492565048 -0.1967535876 -0.0968236047
[121] -0.0281133012 0.1701255198 -0.3593209786 0.4789727612 0.1047447633
[126] 0.6393791654 0.0181489349 -0.1301726680 -0.4121363382 0.2625262411
[131] -0.2845225537 -0.5160331165 -0.6097726651 -0.4966435662 -0.0722821364
[136] 0.5201490125 0.2836630462 0.3694949644 -0.0497482739 -0.0877730709
[141] -0.0159416549 -0.0797782960 0.2238866872 0.0007074616 0.1708424395
[146] -0.4677031532 0.0307980794 -0.1804994674 0.1275394683 0.3876741740
[151] -0.3842320403 -0.4777368682 -0.0813327298 -0.1970028427 -0.5079045248
[156] -0.2125129685 -0.0470725095 -0.1093221997 -0.0221804593 0.5457677672
[161] -0.1810904379 -0.1311928340 0.0172222371 -0.1391953910 0.2189432822
[166] -0.2533260330 -0.0740748349 -0.6116236236 0.5541925416 -0.0951737819
[171] -0.3127929547 0.0859226412 0.5586122379 -0.0345195284 -0.1756852912
[176] 0.3335631253 -1.1047729331 0.0156885329 0.0840894009 0.7431156807
[181] 0.1237652861 0.4501425324 -0.2026614495 -0.0842479012 -0.1142148173
[186] -0.1201001574 -0.1513990247 0.4746604550 -0.2181792150 0.2610967715
[191] 0.3779585127 0.0013168371 -0.0302411715 -0.5230205160 0.2575262168
[196] -0.1760074119 -0.2137335176 -0.4839826358 0.0935614194 0.0252532062
[201] 0.0513676765 -0.3989785596 -0.2286851934 -0.4419247929 -0.4606080065
[206] 0.4419510834 -0.1368144439 -0.5054079177 -0.2094074070 -0.3780766669
[211] -0.0881324786 0.4850286649 -0.2833205574 0.8969624609 -0.3711395620
[216] -0.0108427785 0.2305017827 0.4856821242 -0.0322042588 -0.1750849834
[221] 0.2879268469 -0.1778194051 0.4282428392 -0.4509408458 -0.1282030293
[226] -0.5392732027 0.3255665421 -0.2072947659 -0.2018772391 0.4123258758
>
> proc.time()
user system elapsed
2.007 1.196 3.330
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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: 0xaaaaf10a48e0>
> .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: 0xaaaaf10a48e0>
> .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: 0xaaaaf10a48e0>
> .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: 0xaaaaf10a48e0>
> 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: 0xaaaaf1865270>
> .Call("R_bm_AddColumn",P)
<pointer: 0xaaaaf1865270>
> .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: 0xaaaaf1865270>
> .Call("R_bm_AddColumn",P)
<pointer: 0xaaaaf1865270>
> .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: 0xaaaaf1865270>
> 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: 0xaaaaf1052dc0>
> .Call("R_bm_AddColumn",P)
<pointer: 0xaaaaf1052dc0>
> .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: 0xaaaaf1052dc0>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0xaaaaf1052dc0>
> .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: 0xaaaaf1052dc0>
>
> .Call("R_bm_RowMode",P)
<pointer: 0xaaaaf1052dc0>
> .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: 0xaaaaf1052dc0>
>
> .Call("R_bm_ColMode",P)
<pointer: 0xaaaaf1052dc0>
> .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: 0xaaaaf1052dc0>
> 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: 0xaaaaf18d0370>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0xaaaaf18d0370>
> .Call("R_bm_AddColumn",P)
<pointer: 0xaaaaf18d0370>
> .Call("R_bm_AddColumn",P)
<pointer: 0xaaaaf18d0370>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile2521a33f66d779" "BufferedMatrixFile2521a35f68e8a5"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile2521a33f66d779" "BufferedMatrixFile2521a35f68e8a5"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0xaaaaf3209980>
> .Call("R_bm_AddColumn",P)
<pointer: 0xaaaaf3209980>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0xaaaaf3209980>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0xaaaaf3209980>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0xaaaaf3209980>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0xaaaaf3209980>
> .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: 0xaaaaf2cdffe0>
> .Call("R_bm_AddColumn",P)
<pointer: 0xaaaaf2cdffe0>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0xaaaaf2cdffe0>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0xaaaaf2cdffe0>
> 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: 0xaaaaf3215500>
> .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: 0xaaaaf3215500>
> rm(P)
>
> proc.time()
user system elapsed
0.344 0.036 0.545
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
0.323 0.054 0.364