| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-02-08 01:15:28 -0000 (Wed, 08 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" | 4164 |
| 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 SeqArray package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SeqArray.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 1826/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SeqArray 1.39.2 (landing page) Xiuwen Zheng
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
| Package: SeqArray |
| Version: 1.39.2 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:SeqArray.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings SeqArray_1.39.2.tar.gz |
| StartedAt: 2023-02-07 15:20:49 -0000 (Tue, 07 Feb 2023) |
| EndedAt: 2023-02-07 15:28:52 -0000 (Tue, 07 Feb 2023) |
| EllapsedTime: 483.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: SeqArray.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:SeqArray.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings SeqArray_1.39.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/SeqArray.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 ‘SeqArray/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SeqArray’ version ‘1.39.2’
* 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 ‘SeqArray’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking installed package size ... NOTE
installed size is 6.9Mb
sub-directories of 1Mb or more:
extdata 1.6Mb
libs 4.6Mb
* 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 ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘SeqArray/libs/SeqArray.so’:
Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’,
‘R_WriteConnection’, ‘R_new_custom_connection’
Compiled code should not call non-API entry points in R.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
seqUnitApply 0.318 3.417 20.192
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test.R’
ERROR
Running the tests in ‘tests/test.R’ failed.
Last 13 lines of output:
The following objects are masked from 'package:SeqArray':
alt, filt, fixed, geno, header, info, qual, ref
The following object is masked from 'package:base':
tabulate
[W::bcf_hdr_check_sanity] GL should be declared as Number=G
# of selected variants: 898
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 12s
[..................................................] 0%, ETC: --- Killed
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘OverviewSlides.Rmd’... OK
‘SeqArray.Rmd’ using ‘UTF-8’... OK
‘SeqArrayTutorial.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘OverviewSlides.Rmd’ using rmarkdown
--- finished re-building ‘OverviewSlides.Rmd’
--- re-building ‘SeqArray.Rmd’ using rmarkdown
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
Killed
--- re-building ‘SeqArrayTutorial.Rmd’ using rmarkdown
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
--- finished re-building ‘SeqArrayTutorial.Rmd’
SUMMARY: processing the following file failed:
‘SeqArray.Rmd’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 2 ERRORs, 2 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/SeqArray.Rcheck/00check.log’
for details.
SeqArray.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL SeqArray ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘SeqArray’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.17-bioc/R/library/gdsfmt/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ConvGDS2VCF.cpp -o ConvGDS2VCF.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.17-bioc/R/library/gdsfmt/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ConvToGDS.cpp -o ConvToGDS.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.17-bioc/R/library/gdsfmt/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ConvVCF2GDS.cpp -o ConvVCF2GDS.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.17-bioc/R/library/gdsfmt/include' -I/usr/local/include -fPIC -g -O2 -Wall -c FileMerge.cpp -o FileMerge.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.17-bioc/R/library/gdsfmt/include' -I/usr/local/include -fPIC -g -O2 -Wall -c GetData.cpp -o GetData.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.17-bioc/R/library/gdsfmt/include' -I/usr/local/include -fPIC -g -O2 -Wall -c Index.cpp -o Index.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.17-bioc/R/library/gdsfmt/include' -I/usr/local/include -fPIC -g -O2 -Wall -c LinkSNPRelate.cpp -o LinkSNPRelate.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.17-bioc/R/library/gdsfmt/include' -I/usr/local/include -fPIC -g -O2 -Wall -c Methods.cpp -o Methods.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.17-bioc/R/library/gdsfmt/include' -I/usr/local/include -fPIC -g -O2 -Wall -c R_SeqArray.c -o R_SeqArray.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.17-bioc/R/library/gdsfmt/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ReadBySample.cpp -o ReadBySample.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.17-bioc/R/library/gdsfmt/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ReadByUnit.cpp -o ReadByUnit.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.17-bioc/R/library/gdsfmt/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ReadByVariant.cpp -o ReadByVariant.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.17-bioc/R/library/gdsfmt/include' -I/usr/local/include -fPIC -g -O2 -Wall -c SeqArray.cpp -o SeqArray.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.17-bioc/R/library/gdsfmt/include' -I/usr/local/include -fPIC -g -O2 -Wall -c pkg_test.cpp -o pkg_test.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.17-bioc/R/library/gdsfmt/include' -I/usr/local/include -fPIC -g -O2 -Wall -c samtools_ext.c -o samtools_ext.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.17-bioc/R/library/gdsfmt/include' -I/usr/local/include -fPIC -g -O2 -Wall -c vectorization.c -o vectorization.o g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o SeqArray.so ConvGDS2VCF.o ConvToGDS.o ConvVCF2GDS.o FileMerge.o GetData.o Index.o LinkSNPRelate.o Methods.o R_SeqArray.o ReadBySample.o ReadByUnit.o ReadByVariant.o SeqArray.o pkg_test.o samtools_ext.o vectorization.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-SeqArray/00new/SeqArray/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** 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 (SeqArray)
SeqArray.Rcheck/tests/test.Rout.fail
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.
> if (.Platform$OS.type != "windows")
+ BiocGenerics:::testPackage("SeqArray")
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: 'matrixStats'
The following object is masked from 'package:SeqArray':
rowRanges
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
The following object is masked from 'package:SeqArray':
rowRanges
Loading required package: GenomeInfoDb
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Attaching package: 'SummarizedExperiment'
The following object is masked from 'package:SeqArray':
colData
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Attaching package: 'VariantAnnotation'
The following objects are masked from 'package:SeqArray':
alt, filt, fixed, geno, header, info, qual, ref
The following object is masked from 'package:base':
tabulate
[W::bcf_hdr_check_sanity] GL should be declared as Number=G
# of selected variants: 898
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 12s
[..................................................] 0%, ETC: --- Killed
SeqArray.Rcheck/SeqArray-Ex.timings
| name | user | system | elapsed | |
| SeqArray-package | 0.449 | 0.032 | 0.624 | |
| SeqVarGDSClass-class | 0.172 | 0.012 | 0.266 | |
| seqAddValue | 0.177 | 0.020 | 0.196 | |
| seqAlleleFreq | 0.058 | 0.012 | 0.071 | |
| seqApply | 0.135 | 0.016 | 0.194 | |
| seqAsVCF | 0.003 | 0.000 | 0.003 | |
| seqBED2GDS | 0.333 | 0.055 | 0.621 | |
| seqBlockApply | 0.076 | 0.008 | 0.084 | |
| seqCheck | 0.037 | 0.000 | 0.038 | |
| seqDelete | 0.126 | 0.004 | 0.129 | |
| seqDigest | 0.023 | 0.000 | 0.024 | |
| seqEmptyFile | 0.024 | 0.000 | 0.023 | |
| seqExampleFileName | 0.002 | 0.000 | 0.002 | |
| seqExport | 0.692 | 0.135 | 0.856 | |
| seqGDS2SNP | 0.057 | 0.020 | 0.078 | |
| seqGDS2VCF | 0.797 | 0.020 | 0.872 | |
| seqGet2bGeno | 0.007 | 0.004 | 0.011 | |
| seqGetData | 1.878 | 0.016 | 2.092 | |
| seqGetFilter | 0.062 | 0.004 | 0.066 | |
| seqMerge | 0.825 | 0.096 | 0.976 | |
| seqMissing | 0.089 | 0.004 | 0.093 | |
| seqNewVarData | 0.003 | 0.000 | 0.003 | |
| seqNumAllele | 0.003 | 0.000 | 0.003 | |
| seqOpen | 0.613 | 0.004 | 0.617 | |
| seqOptimize | 0.207 | 0.004 | 0.294 | |
| seqParallel | 0.130 | 0.496 | 0.542 | |
| seqParallelSetup | 0.073 | 0.123 | 0.195 | |
| seqRecompress | 0.316 | 0.061 | 0.371 | |
| seqResetVariantID | 0.022 | 0.008 | 0.030 | |
| seqSNP2GDS | 1.486 | 0.066 | 2.047 | |
| seqSetFilter | 0.079 | 0.028 | 0.180 | |
| seqSetFilterCond | 0.066 | 0.012 | 0.078 | |
| seqStorageOption | 0.666 | 0.099 | 0.983 | |
| seqSummary | 0.147 | 0.020 | 0.337 | |
| seqSystem | 0.001 | 0.000 | 0.000 | |
| seqTranspose | 0.236 | 0.020 | 0.327 | |
| seqUnitApply | 0.318 | 3.417 | 20.192 | |
| seqUnitFilterCond | 0.079 | 0.008 | 0.157 | |
| seqUnitSlidingWindows | 0.046 | 0.004 | 0.090 | |
| seqUnitSubset | 0.060 | 0.016 | 0.141 | |
| seqVCF2GDS | 0.646 | 0.354 | 1.049 | |
| seqVCF_Header | 0.110 | 0.008 | 0.118 | |
| seqVCF_SampID | 0.002 | 0.000 | 0.002 | |