Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 1948/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ShortRead 1.64.0 (landing page) Bioconductor Package Maintainer
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
To the developers/maintainers of the ShortRead package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ShortRead.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: ShortRead |
Version: 1.64.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ShortRead.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ShortRead_1.64.0.tar.gz |
StartedAt: 2024-12-20 05:59:44 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 06:09:49 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 605.0 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: ShortRead.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ShortRead.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ShortRead_1.64.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/ShortRead.Rcheck' * using R version 4.4.2 (2024-10-31 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'ShortRead/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'ShortRead' version '1.64.0' * 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 whether package 'ShortRead' can be installed ... WARNING Found the following significant warnings: io.c:227:38: warning: format '%f' expects argument of type 'double', but argument 2 has type 'const char *' [-Wformat=] io.c:658:49: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'int' [-Wformat=] io.c:676:48: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'int' [-Wformat=] maqmap_m.h:102:21: warning: pointer 'mm' used after 'void free(void*)' [-Wuse-after-free] See 'F:/biocbuild/bbs-3.20-bioc/meat/ShortRead.Rcheck/00install.out' for details. * used C compiler: 'gcc.exe (GCC) 13.3.0' * used C++ compiler: 'G__~1.EXE (GCC) 13.3.0' * checking installed package size ... NOTE installed size is 7.4Mb sub-directories of 1Mb or more: R 2.2Mb extdata 4.0Mb * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... NOTE Unexported object imported by a ':::' call: 'S4Vectors:::V_recycle' 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 ... NOTE .plotCycleBaseCall: no visible binding for global variable 'Base' flag,QAReadQuality: no visible binding for global variable 'Score' flag,QAReadQuality: no visible binding for global variable 'Id' flag,QAReadQuality: no visible binding for global variable 'Density' report,QAFrequentSequence: no visible binding for global variable 'TopCount' report,QAFrequentSequence: no visible binding for global variable 'Id' report,QANucleotideByCycle: no visible binding for global variable 'Base' report,QANucleotideUse: no visible binding for global variable 'Nucleotide' report,QAQualityUse: no visible binding for global variable 'Count' report,QAQualityUse: no visible binding for global variable 'Id' report,QAQualityUse: no visible binding for global variable 'Quality' report,QAReadQuality: no visible binding for global variable 'Id' report,QASequenceUse: no visible binding for global variable 'Occurrences' report,QASequenceUse: no visible binding for global variable 'Id' report,QASequenceUse: no visible binding for global variable 'Reads' Undefined global functions or variables: Base Count Density Id Nucleotide Occurrences Quality Reads Score TopCount * checking Rd files ... NOTE checkRd: (-1) deprecated.Rd:21: Lost braces in \itemize; meant \describe ? checkRd: (-1) deprecated.Rd:23-24: Lost braces in \itemize; meant \describe ? * checking Rd metadata ... NOTE Invalid package aliases in Rd file 'ShortRead-package.Rd': 'ShortReadBase-package' * 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 shell scripts ... 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 for x64 is not available File 'F:/biocbuild/bbs-3.20-bioc/R/library/ShortRead/libs/x64/ShortRead.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (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 nor [v]sprintf. 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 files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed Snapshot-class 6.88 0.32 7.22 srdistance 3.28 0.08 39.19 readBaseQuality 3.10 0.01 13.95 readPrb 1.11 0.00 13.20 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'ShortRead_unit_tests.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 6 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/ShortRead.Rcheck/00check.log' for details.
ShortRead.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL ShortRead ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'ShortRead' ... ** using staged installation ********************************************** WARNING: this package has a configure script It probably needs manual configuration ********************************************** ** libs using C compiler: 'gcc.exe (GCC) 13.3.0' using C++ compiler: 'G__~1.EXE (GCC) 13.3.0' gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Biostrings_stubs.c -o Biostrings_stubs.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_init_ShortRead.c -o R_init_ShortRead.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c XVector_stubs.c -o XVector_stubs.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c alphabet.c -o alphabet.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c count.c -o count.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c io.c -o io.o io.c: In function 'read_prb_as_character': io.c:227:38: warning: format '%f' expects argument of type 'double', but argument 2 has type 'const char *' [-Wformat=] 227 | error("could not read file '%f'", translateChar(STRING_ELT(fname, 0))); | ~^ | | | double | %s io.c: In function '_read_solexa_export_file': io.c:658:49: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'int' [-Wformat=] 658 | error("invalid 'strand' field '%s', %s:%d", | ~^ | | | char * | %d 659 | *elt[13], fname, lineno); | ~~~~~~~~ | | | int io.c:676:48: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'int' [-Wformat=] 676 | error("invalid 'filtering' field '%s', %s:%d", | ~^ | | | char * | %d 677 | *elt[21], fname, lineno); | ~~~~~~~~ | | | int gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c io_bowtie.c -o io_bowtie.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c io_soap.c -o io_soap.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c readBfaToc.cc -o readBfaToc.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c read_maq_map.cc -o read_maq_map.o In file included from read_maq_map.cc:13: maqmap_m.h: In function 'maqmap_T<max_readlen>* maqmap_read_header(gzFile) [with int max_readlen = 128]': maqmap_m.h:102:21: warning: pointer 'mm' used after 'void free(void*)' [-Wuse-after-free] 102 | Rf_error("MAQ format '%d' not supported", mm->format); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void maq_delete_maqmap(maqmap_T<max_readlen>*) [with int max_readlen = 128]', inlined from 'void maq_delete_maqmap(maqmap_T<max_readlen>*) [with int max_readlen = 128]' at maqmap_m.h:74:35, inlined from 'maqmap_T<max_readlen>* maqmap_read_header(gzFile) [with int max_readlen = 128]' at maqmap_m.h:101:30: maqmap_m.h:84:14: note: call to 'void free(void*)' here 84 | std::free(mm); | ~~~~~~~~~^~~~ maqmap_m.h: In function 'maqmap_T<max_readlen>* maqmap_read_header(gzFile) [with int max_readlen = 64]': maqmap_m.h:102:21: warning: pointer 'mm' used after 'void free(void*)' [-Wuse-after-free] 102 | Rf_error("MAQ format '%d' not supported", mm->format); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void maq_delete_maqmap(maqmap_T<max_readlen>*) [with int max_readlen = 64]', inlined from 'void maq_delete_maqmap(maqmap_T<max_readlen>*) [with int max_readlen = 64]' at maqmap_m.h:74:35, inlined from 'maqmap_T<max_readlen>* maqmap_read_header(gzFile) [with int max_readlen = 64]' at maqmap_m.h:101:30: maqmap_m.h:84:14: note: call to 'void free(void*)' here 84 | std::free(mm); | ~~~~~~~~~^~~~ gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sampler.c -o sampler.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c trim.c -o trim.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c util.c -o util.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c xsnap.c -o xsnap.o g++ -std=gnu++17 -shared -s -static-libgcc -o ShortRead.dll tmp.def Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.o S4Vectors_stubs.o XVector_stubs.o alphabet.o count.o io.o io_bowtie.o io_soap.o readBfaToc.o read_maq_map.o sampler.o trim.o util.o xsnap.o -lz -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-ShortRead/00new/ShortRead/libs/x64 ** R ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ShortRead)
ShortRead.Rcheck/tests/ShortRead_unit_tests.Rout
R version 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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. > BiocGenerics:::testPackage("ShortRead") 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, saveRDS, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit 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 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 RUNIT TEST PROTOCOL -- Fri Dec 20 06:09:32 2024 *********************************************** Number of test functions: 106 Number of errors: 0 Number of failures: 0 1 Test Suite : ShortRead RUnit Tests - 106 test functions, 0 errors, 0 failures Number of test functions: 106 Number of errors: 0 Number of failures: 0 Warning message: In .Internal(gc(verbose, reset, full)) : closing unused connection 3 (F:\biocbuild\bbs-3.20-bioc\tmpdir\Rtmpi4s2Fy\file129202dfc6779) > > proc.time() user system elapsed 28.39 2.81 221.01
ShortRead.Rcheck/ShortRead-Ex.timings
name | user | system | elapsed | |
AlignedRead-class | 0.45 | 0.06 | 0.53 | |
BowtieQA-class | 0 | 0 | 0 | |
ExperimentPath-class | 0 | 0 | 0 | |
FastqQA-class | 0.01 | 0.00 | 0.01 | |
Intensity-class | 0.17 | 0.02 | 0.27 | |
MAQMapQA-class | 0 | 0 | 0 | |
QA-class | 0 | 0 | 0 | |
QualityScore-class | 0.02 | 0.00 | 0.01 | |
QualityScore | 0 | 0 | 0 | |
RochePath-class | 0 | 0 | 0 | |
RocheSet-class | 0 | 0 | 0 | |
RtaIntensity-class | 0.05 | 0.00 | 0.04 | |
RtaIntensity | 0.03 | 0.00 | 0.04 | |
SRFilter-class | 0 | 0 | 0 | |
SRFilterResult-class | 0.06 | 0.00 | 0.06 | |
SRSet-class | 0 | 0 | 0 | |
SRUtil-class | 0.02 | 0.00 | 0.02 | |
Sampler-class | 1.03 | 0.05 | 1.09 | |
ShortRead-class | 0.06 | 0.00 | 0.07 | |
ShortReadQ-class | 0.25 | 0.04 | 0.29 | |
Snapshot-class | 6.88 | 0.32 | 7.22 | |
SnapshotFunction-class | 0 | 0 | 0 | |
SolexaExportQA-class | 0 | 0 | 0 | |
SolexaIntensity-class | 0.06 | 0.01 | 0.08 | |
SolexaPath-class | 0.06 | 0.02 | 0.08 | |
SolexaSet-class | 0.05 | 0.00 | 0.05 | |
SpTrellis-class | 0.29 | 0.03 | 0.33 | |
accessors | 0 | 0 | 0 | |
alphabetByCycle | 0.04 | 0.02 | 0.05 | |
clean | 0 | 0 | 0 | |
countLines | 0.10 | 0.03 | 0.29 | |
dotQA-class | 0 | 0 | 0 | |
dustyScore | 0.08 | 0.00 | 0.08 | |
filterFastq | 1.06 | 0.03 | 1.09 | |
polyn | 0 | 0 | 0 | |
qa | 0.39 | 0.07 | 0.45 | |
qa2 | 3.22 | 0.29 | 3.83 | |
readAligned | 0.28 | 0.02 | 0.30 | |
readBaseQuality | 3.10 | 0.01 | 13.95 | |
readFasta | 0.07 | 0.02 | 0.14 | |
readFastq | 0.14 | 0.01 | 0.17 | |
readIntensities | 0.1 | 0.0 | 0.1 | |
readPrb | 1.11 | 0.00 | 13.20 | |
readQseq | 0.01 | 0.00 | 0.02 | |
readXStringColumns | 0.08 | 0.04 | 0.11 | |
renew | 0.06 | 0.00 | 0.06 | |
report | 0.02 | 0.00 | 0.01 | |
spViewPerFeature | 2.98 | 0.15 | 3.14 | |
srFilter | 0.22 | 0.03 | 0.25 | |
srdistance | 3.28 | 0.08 | 39.19 | |
srduplicated | 0.03 | 0.02 | 0.05 | |
tables | 0.13 | 0.00 | 0.12 | |
trimTails | 0.02 | 0.01 | 0.03 | |