| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-04-17 11:37:19 -0400 (Wed, 17 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
| 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 1943/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ShortRead 1.60.0 (landing page) Bioconductor Package Maintainer
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
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: 1.60.0 |
| Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ShortRead.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings ShortRead_1.60.0.tar.gz |
| StartedAt: 2024-04-16 05:07:02 -0400 (Tue, 16 Apr 2024) |
| EndedAt: 2024-04-16 05:16:35 -0400 (Tue, 16 Apr 2024) |
| EllapsedTime: 572.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ShortRead.Rcheck |
| Warnings: 1 |
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### Running command:
###
### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ShortRead.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings ShortRead_1.60.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/ShortRead.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 12.3.0
GNU Fortran (GCC) 12.3.0
* 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 '1.60.0'
* 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:
maqmap_m.h:102:18: warning: pointer 'mm' used after 'void free(void*)' [-Wuse-after-free]
See 'F:/biocbuild/bbs-3.18-bioc/meat/ShortRead.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
* used C++ compiler: 'G__~1.EXE (GCC) 12.3.0'
* checking installed package size ... NOTE
installed size is 7.3Mb
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 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 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 ... 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 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-3.18-bioc/R/library/ShortRead/libs/x64/ShortRead.dll':
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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
Snapshot-class 6.47 0.35 6.82
srdistance 3.33 0.07 36.52
readBaseQuality 2.83 0.03 14.58
readPrb 1.13 0.04 12.22
* 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 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: 1 WARNING, 4 NOTEs
See
'F:/biocbuild/bbs-3.18-bioc/meat/ShortRead.Rcheck/00check.log'
for details.
ShortRead.Rcheck/00install.out
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### Running command:
###
### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL ShortRead
###
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* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/library'
* installing *source* package 'ShortRead' ...
** using staged installation
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
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** libs
using C compiler: 'gcc.exe (GCC) 12.3.0'
using C++ compiler: 'G__~1.EXE (GCC) 12.3.0'
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I"C:/rtools43/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-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I"C:/rtools43/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-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I"C:/rtools43/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-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I"C:/rtools43/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-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I"C:/rtools43/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-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c alphabet.c -o alphabet.o
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c count.c -o count.o
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c io.c -o io.o
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I"C:/rtools43/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-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I"C:/rtools43/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-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I"C:/rtools43/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-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I"C:/rtools43/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(bioc_gzFile) [with int max_readlen = 128]':
maqmap_m.h:102:18: warning: pointer 'mm' used after 'void free(void*)' [-Wuse-after-free]
102 | 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(bioc_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(bioc_gzFile) [with int max_readlen = 64]':
maqmap_m.h:102:18: warning: pointer 'mm' used after 'void free(void*)' [-Wuse-after-free]
102 | 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(bioc_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-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sampler.c -o sampler.o
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c trim.c -o trim.o
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c util.c -o util.o
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I"C:/rtools43/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 -LF:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.18-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.18-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 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake"
Copyright (C) 2024 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.
> 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, setdiff, sort, 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 -- Tue Apr 16 05:16:16 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-3.18-bioc\tmpdir\Rtmpw3sK7C\file14e404b871c89)
>
> proc.time()
user system elapsed
27.50 1.75 212.26
ShortRead.Rcheck/ShortRead-Ex.timings
| name | user | system | elapsed | |
| AlignedRead-class | 0.27 | 0.05 | 0.31 | |
| BowtieQA-class | 0 | 0 | 0 | |
| ExperimentPath-class | 0 | 0 | 0 | |
| FastqQA-class | 0 | 0 | 0 | |
| Intensity-class | 1.00 | 0.00 | 1.01 | |
| MAQMapQA-class | 0 | 0 | 0 | |
| QA-class | 0 | 0 | 0 | |
| QualityScore-class | 0.01 | 0.00 | 0.01 | |
| QualityScore | 0 | 0 | 0 | |
| RochePath-class | 0 | 0 | 0 | |
| RocheSet-class | 0.02 | 0.00 | 0.02 | |
| RtaIntensity-class | 0.06 | 0.00 | 0.06 | |
| RtaIntensity | 0.03 | 0.00 | 0.03 | |
| SRFilter-class | 0 | 0 | 0 | |
| SRFilterResult-class | 0.07 | 0.00 | 0.06 | |
| SRSet-class | 0 | 0 | 0 | |
| SRUtil-class | 0 | 0 | 0 | |
| Sampler-class | 1.11 | 0.00 | 1.13 | |
| ShortRead-class | 0.04 | 0.00 | 0.04 | |
| ShortReadQ-class | 0.22 | 0.00 | 0.22 | |
| Snapshot-class | 6.47 | 0.35 | 6.82 | |
| SnapshotFunction-class | 0 | 0 | 0 | |
| SolexaExportQA-class | 0 | 0 | 0 | |
| SolexaIntensity-class | 0.08 | 0.00 | 0.11 | |
| SolexaPath-class | 0.09 | 0.00 | 0.09 | |
| SolexaSet-class | 0.1 | 0.0 | 0.1 | |
| SpTrellis-class | 0.43 | 0.04 | 0.47 | |
| accessors | 0.02 | 0.00 | 0.01 | |
| alphabetByCycle | 0.02 | 0.00 | 0.02 | |
| clean | 0.01 | 0.00 | 0.01 | |
| countLines | 0.13 | 0.00 | 0.16 | |
| dotQA-class | 0 | 0 | 0 | |
| dustyScore | 0.17 | 0.00 | 0.17 | |
| filterFastq | 1.09 | 0.01 | 1.13 | |
| polyn | 0 | 0 | 0 | |
| qa | 0.39 | 0.00 | 0.39 | |
| qa2 | 3.06 | 0.37 | 3.61 | |
| readAligned | 0.21 | 0.03 | 0.27 | |
| readBaseQuality | 2.83 | 0.03 | 14.58 | |
| readFasta | 0.11 | 0.00 | 0.12 | |
| readFastq | 0.12 | 0.00 | 0.14 | |
| readIntensities | 0.06 | 0.00 | 0.09 | |
| readPrb | 1.13 | 0.04 | 12.22 | |
| readQseq | 0.01 | 0.00 | 0.02 | |
| readXStringColumns | 0.02 | 0.03 | 0.06 | |
| renew | 0.03 | 0.00 | 0.03 | |
| report | 0 | 0 | 0 | |
| spViewPerFeature | 2.91 | 0.18 | 3.10 | |
| srFilter | 0.31 | 0.04 | 0.34 | |
| srdistance | 3.33 | 0.07 | 36.52 | |
| srduplicated | 0.06 | 0.00 | 0.06 | |
| tables | 0.12 | 0.02 | 0.14 | |
| trimTails | 0.05 | 0.00 | 0.05 | |