Hervé Pagès
| Snapshot Date: 2022-09-29 14:00:03 -0400 (Thu, 29 Sep 2022) |
| git_url: https://git.bioconductor.org/packages/DelayedArray |
| git_branch: master |
| git_last_commit: acb817e |
| git_last_commit_date: 2022-09-13 18:08:26 -0400 (Tue, 13 Sep 2022) |
| Back to Multiple platform build/check report for BioC 3.16 |
|
This page was generated on 2022-09-30 11:07:20 -0400 (Fri, 30 Sep 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4428 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4206 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.1 Patched (2022-07-09 r82577) -- "Funny-Looking Kid" | 4222 |
| 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 DelayedArray package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DelayedArray.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 498/2157 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DelayedArray 0.23.2 (landing page) Hervé Pagès
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: DelayedArray |
| Version: 0.23.2 |
| Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DelayedArray.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings DelayedArray_0.23.2.tar.gz |
| StartedAt: 2022-09-30 00:22:13 -0400 (Fri, 30 Sep 2022) |
| EndedAt: 2022-09-30 00:36:05 -0400 (Fri, 30 Sep 2022) |
| EllapsedTime: 831.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: DelayedArray.Rcheck |
| Warnings: 3 |
##############################################################################
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###
### Running command:
###
### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DelayedArray.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings DelayedArray_0.23.2.tar.gz
###
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##############################################################################
* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/DelayedArray.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'DelayedArray/DESCRIPTION' ... OK
* this is package 'DelayedArray' version '0.23.2'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'stats4', 'Matrix', 'BiocGenerics', 'MatrixGenerics', 'S4Vectors',
'IRanges'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 whether package 'DelayedArray' can be installed ... WARNING
Found the following significant warnings:
compress_atomic_vector.c:66:9: warning: 'ans' is used uninitialized in this function [-Wuninitialized]
compress_atomic_vector.c:73:9: warning: 'ans' is used uninitialized in this function [-Wuninitialized]
compress_atomic_vector.c:85:9: warning: 'ans' is used uninitialized in this function [-Wuninitialized]
compress_atomic_vector.c:92:9: warning: 'ans' is used uninitialized in this function [-Wuninitialized]
See 'F:/biocbuild/bbs-3.16-bioc/meat/DelayedArray.Rcheck/00install.out' for details.
* 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 ... WARNING
Subdirectory 'inst/doc' contains invalid file names:
'02-Implementing_a_backend.Rmd' '01-Working_with_large_arrays.Rnw'
'03-DelayedArray_HDF5Array_update.Rnw'
'02-Implementing_a_backend.html' '01-Working_with_large_arrays.pdf'
'03-DelayedArray_HDF5Array_update.pdf'
Please remove or rename the files.
See section 'Package subdirectories' in the 'Writing R Extensions'
manual.
* 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 ... NOTE
Unexported objects imported by ':::' calls:
'BiocGenerics:::replaceSlots' 'BiocGenerics:::testPackage'
'S4Vectors:::.list.names' 'S4Vectors:::anyMissing'
'S4Vectors:::anyMissingOrOutside' 'S4Vectors:::delete_NULLs'
'S4Vectors:::diffWithInitialZero'
'S4Vectors:::extract_positions_from_Rle' 'S4Vectors:::new_DataFrame'
'S4Vectors:::sapply_isNULL'
See the note in ?`:::` about the use of this operator.
* 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 ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
'defaultMultAutoGrids' 'multGrids'
Undocumented S4 methods:
generic '[' and siglist 'DelayedArray,ANY,ANY,ANY'
generic '[<-' and siglist 'DelayedArray,ANY,ANY,ANY'
generic 'crossprod' and siglist 'ANY,DelayedMatrix'
generic 'crossprod' and siglist 'DelayedMatrix,ANY'
generic 'crossprod' and siglist 'DelayedMatrix,DelayedMatrix'
generic 'crossprod' and siglist 'DelayedMatrix,missing'
generic 'tcrossprod' and siglist 'ANY,DelayedMatrix'
generic 'tcrossprod' and siglist 'DelayedMatrix,ANY'
generic 'tcrossprod' and siglist 'DelayedMatrix,DelayedMatrix'
generic 'tcrossprod' and siglist 'DelayedMatrix,missing'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 for x64 is not available
File 'F:/biocbuild/bbs-3.16-bioc/R/library/DelayedArray/libs/x64/DelayedArray.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking sizes of PDF files under 'inst/doc' ... NOTE
'qpdf' made some significant size reductions:
compacted '01-Working_with_large_arrays.pdf' from 525Kb to 256Kb
consider running tools::compactPDF() on these files
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
RleArray-class 46.50 2.81 49.47
DelayedMatrix-utils 18.61 1.15 20.13
DelayedArray-utils 9.86 0.57 10.60
sparseMatrix-utils 8.77 0.23 9.00
DelayedArray-class 6.92 0.29 7.59
blockApply 1.41 0.14 9.65
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'run_unitTests.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: 3 WARNINGs, 4 NOTEs
See
'F:/biocbuild/bbs-3.16-bioc/meat/DelayedArray.Rcheck/00check.log'
for details.
DelayedArray.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.16/bioc/src/contrib/DelayedArray_0.23.2.tar.gz && rm -rf DelayedArray.buildbin-libdir && mkdir DelayedArray.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DelayedArray.buildbin-libdir DelayedArray_0.23.2.tar.gz && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL DelayedArray_0.23.2.zip && rm DelayedArray_0.23.2.tar.gz DelayedArray_0.23.2.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 185k 100 185k 0 0 2517k 0 --:--:-- --:--:-- --:--:-- 2541k
only one architecture so ignoring '--merge-multiarch'
* installing *source* package 'DelayedArray' ...
** using staged installation
** libs
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_DelayedArray.c -o R_init_DelayedArray.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c abind.c -o abind.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c array_selection.c -o array_selection.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c compress_atomic_vector.c -o compress_atomic_vector.o
compress_atomic_vector.c: In function 'C_encode_atomic_vector':
compress_atomic_vector.c:66:9: warning: 'ans' is used uninitialized in this function [-Wuninitialized]
66 | return ans;
| ^~~
compress_atomic_vector.c: In function 'C_decode_atomic_vector':
compress_atomic_vector.c:73:9: warning: 'ans' is used uninitialized in this function [-Wuninitialized]
73 | return ans;
| ^~~
compress_atomic_vector.c: In function 'C_compress_atomic_vector':
compress_atomic_vector.c:85:9: warning: 'ans' is used uninitialized in this function [-Wuninitialized]
85 | return ans;
| ^~~
compress_atomic_vector.c: In function 'C_decompress_atomic_vector':
compress_atomic_vector.c:92:9: warning: 'ans' is used uninitialized in this function [-Wuninitialized]
92 | return ans;
| ^~~
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sparseMatrix_utils.c -o sparseMatrix_utils.o
gcc -shared -s -static-libgcc -o DelayedArray.dll tmp.def R_init_DelayedArray.o S4Vectors_stubs.o abind.o array_selection.o compress_atomic_vector.o sparseMatrix_utils.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.16-bioc/meat/DelayedArray.buildbin-libdir/00LOCK-DelayedArray/00new/DelayedArray/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'rowsum' in package 'DelayedArray'
Creating a new generic function for 'apply' in package 'DelayedArray'
Creating a new generic function for 'sweep' in package 'DelayedArray'
Creating a new generic function for 'scale' in package 'DelayedArray'
Creating a generic function for 'dnorm' from package 'stats' in package 'DelayedArray'
Creating a generic function for 'pnorm' from package 'stats' in package 'DelayedArray'
Creating a generic function for 'qnorm' from package 'stats' in package 'DelayedArray'
Creating a generic function for 'dbinom' from package 'stats' in package 'DelayedArray'
Creating a generic function for 'pbinom' from package 'stats' in package 'DelayedArray'
Creating a generic function for 'qbinom' from package 'stats' in package 'DelayedArray'
Creating a generic function for 'dpois' from package 'stats' in package 'DelayedArray'
Creating a generic function for 'ppois' from package 'stats' in package 'DelayedArray'
Creating a generic function for 'qpois' from package 'stats' in package 'DelayedArray'
Creating a generic function for 'dlogis' from package 'stats' in package 'DelayedArray'
Creating a generic function for 'plogis' from package 'stats' in package 'DelayedArray'
Creating a generic function for 'qlogis' from package 'stats' in package 'DelayedArray'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'DelayedArray' as DelayedArray_0.23.2.zip
* DONE (DelayedArray)
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
package 'DelayedArray' successfully unpacked and MD5 sums checked
DelayedArray.Rcheck/tests/run_unitTests.Rout
R version 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.
> require("DelayedArray") || stop("unable to load DelayedArray package")
Loading required package: DelayedArray
Loading required package: stats4
Loading required package: Matrix
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:Matrix':
expand, unname
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Attaching package: 'DelayedArray'
The following objects are masked from 'package:base':
apply, rowsum, scale, sweep
[1] TRUE
> DelayedArray:::.test()
Attaching package: 'genefilter'
The following objects are masked from 'package:MatrixGenerics':
rowSds, rowVars
The following objects are masked from 'package:matrixStats':
rowSds, rowVars
Loading required package: stats4
Loading required package: Matrix
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:Matrix':
expand, unname
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Attaching package: 'DelayedArray'
The following objects are masked from 'package:base':
apply, rowsum, scale, sweep
Loading required package: stats4
Loading required package: Matrix
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:Matrix':
expand, unname
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Attaching package: 'DelayedArray'
The following objects are masked from 'package:base':
apply, rowsum, scale, sweep
Loading required package: stats4
Loading required package: Matrix
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:Matrix':
expand, unname
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Attaching package: 'DelayedArray'
The following objects are masked from 'package:base':
apply, rowsum, scale, sweep
Loading required package: stats4
Loading required package: Matrix
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:Matrix':
expand, unname
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Attaching package: 'DelayedArray'
The following objects are masked from 'package:base':
apply, rowsum, scale, sweep
Error in normarg_perm(perm, dim(seed)) : 'perm' must be an integer vector
In addition: Warning messages:
1: In log(a + 0.2) : NaNs produced
2: In OP(a) : NaNs produced
3: Argument 'center' should be of the same length as number of rows of 'x'. Use of a scalar value is deprecated: 1 != 8
4: Argument 'center' should be of the same length as number of rows of 'x'. Use of a scalar value is deprecated: 1 != 8
5: Argument 'center' should be of the same length as number of rows of 'x'. Use of a scalar value is deprecated: 1 != 8
Error in validObject(.Object) : invalid class "DelayedAperm" object:
'perm' cannot be an empty vector
Error in validObject(.Object) : invalid class "DelayedAperm" object:
only dimensions equal to 1 can be dropped
Error in validObject(.Object) : invalid class "DelayedAperm" object:
all non-NA values in 'perm' must be >= 1 and <= 'length(dim(a))'
Error in validObject(.Object) : invalid class "DelayedAperm" object:
only dimensions equal to 1 can be dropped
Error in seed(x) :
seed() is not supported on a DelayedArray object with multiple seeds at
the moment. Note that you can check the number of seeds with nseed().
You can use 'seedApply(x, identity)' to extract all the seeds as a
list.
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'is_noop' for signature '"DelayedNaryIsoOp"'
Error in seed(x) :
seed() is not supported on a DelayedArray object with multiple seeds at
the moment. Note that you can check the number of seeds with nseed().
You can use 'seedApply(x, identity)' to extract all the seeds as a
list.
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'is_noop' for signature '"DelayedNaryIsoOp"'
Error in seed(x) :
seed() is not supported on a DelayedArray object with multiple seeds at
the moment. Note that you can check the number of seeds with nseed().
You can use 'seedApply(x, identity)' to extract all the seeds as a
list.
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'is_noop' for signature '"DelayedNaryIsoOp"'
Error in seed(x) :
seed() is not supported on a DelayedArray object with multiple seeds at
the moment. Note that you can check the number of seeds with nseed().
You can use 'seedApply(x, identity)' to extract all the seeds as a
list.
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'is_noop' for signature '"DelayedNaryIsoOp"'
Error in seed(x) :
seed() is not supported on a DelayedArray object with multiple seeds at
the moment. Note that you can check the number of seeds with nseed().
You can use 'seedApply(x, identity)' to extract all the seeds as a
list.
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'is_noop' for signature '"DelayedNaryIsoOp"'
Error in match.fun(OP) : 'NULL' is not a function, character or symbol
Error in match.fun(OP) :
'list(NULL)' is not a function, character or symbol
Error in get(as.character(FUN), mode = "function", envir = envir) :
object 'not-an-existing-function' of mode 'function' was not found
Error in new_DelayedNaryIsoOp("<=", array(dim = 4:2), array(dim = 2:4)) :
non-conformable array-like objects
Error in normarg_dimnames(dimnames, seed_dim) :
the supplied 'dimnames' must be NULL or a list
Error in normarg_dimnames(dimnames, seed_dim) :
the supplied 'dimnames' must have one list element per dimension
Error in FUN(X[[i]], ...) :
each list element in the supplied 'dimnames' must be NULL or a
character vector
Error in FUN(X[[i]], ...) :
length of 'dimnames[[1]]' (26) must equal the array extent (5)
Error in normalizeNindex(Nindex, seed) :
'Nindex' must be a list with one list element per dimension in 'x'
Error in normalizeNindex(Nindex, seed) :
'Nindex' must be a list with one list element per dimension in 'x'
Error : subscript contains out-of-bounds indices
Error : subscript contains invalid names
Error : subscript contains out-of-bounds ranges
Error : subscript contains out-of-bounds ranges
Error in new_DelayedUnaryIsoOpStack(.TEST_SAS3, NULL) :
'OPS' must be a list
Error in FUN(X[[i]], ...) :
'OPS[[1L]]' is not a function, character or symbol
Error in get(as.character(FUN), mode = "function", envir = envir) :
object 'not-an-existing-function' of mode 'function' was not found
RUNIT TEST PROTOCOL -- Fri Sep 30 00:35:52 2022
***********************************************
Number of test functions: 55
Number of errors: 0
Number of failures: 0
1 Test Suite :
DelayedArray RUnit Tests - 55 test functions, 0 errors, 0 failures
Number of test functions: 55
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
550.75 6.18 593.29
DelayedArray.Rcheck/DelayedArray-Ex.timings
| name | user | system | elapsed | |
| Array-class | 0 | 0 | 0 | |
| ArrayGrid-class | 0.70 | 0.01 | 0.72 | |
| AutoBlock-global-settings | 0.14 | 0.00 | 0.14 | |
| AutoGrid | 1.16 | 0.07 | 1.31 | |
| ConstantArray-class | 0.14 | 0.00 | 0.14 | |
| DelayedAbind-class | 0.09 | 0.03 | 0.11 | |
| DelayedAperm-class | 0.05 | 0.00 | 0.05 | |
| DelayedArray-class | 6.92 | 0.29 | 7.59 | |
| DelayedArray-stats | 1.95 | 0.11 | 2.08 | |
| DelayedArray-utils | 9.86 | 0.57 | 10.60 | |
| DelayedMatrix-stats | 2.44 | 0.46 | 2.90 | |
| DelayedMatrix-utils | 18.61 | 1.15 | 20.13 | |
| DelayedNaryIsoOp-class | 0.06 | 0.00 | 0.06 | |
| DelayedSetDimnames-class | 0.01 | 0.00 | 0.01 | |
| DelayedSubassign-class | 0.10 | 0.01 | 0.11 | |
| DelayedSubset-class | 0.06 | 0.00 | 0.06 | |
| DelayedUnaryIsoOpStack-class | 0.06 | 0.00 | 0.07 | |
| DelayedUnaryIsoOpWithArgs-class | 0.10 | 0.05 | 0.14 | |
| RleArray-class | 46.50 | 2.81 | 49.47 | |
| SparseArraySeed-class | 0.31 | 0.05 | 0.36 | |
| SparseArraySeed-utils | 0.02 | 0.00 | 0.02 | |
| array_selection | 0 | 0 | 0 | |
| bind-arrays | 0 | 0 | 0 | |
| blockApply | 1.41 | 0.14 | 9.65 | |
| chunkGrid | 0 | 0 | 0 | |
| extract_array | 0 | 0 | 0 | |
| makeCappedVolumeBox | 0.20 | 0.01 | 0.22 | |
| mapToGrid | 0.01 | 0.00 | 0.02 | |
| read_block | 0.07 | 0.00 | 0.06 | |
| realize | 2.47 | 0.14 | 2.76 | |
| showtree | 0.12 | 0.00 | 0.13 | |
| simplify | 0.34 | 0.02 | 0.36 | |
| sparseMatrix-utils | 8.77 | 0.23 | 9.00 | |
| write_block | 2.98 | 0.41 | 3.86 | |