| Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-01-02 09:00:29 -0500 (Mon, 02 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
| 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 FastqCleaner package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 650/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| FastqCleaner 1.17.0 (landing page) Leandro Roser
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ||||||||
| Package: FastqCleaner |
| Version: 1.17.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:FastqCleaner.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings FastqCleaner_1.17.0.tar.gz |
| StartedAt: 2022-12-28 23:44:45 -0500 (Wed, 28 Dec 2022) |
| EndedAt: 2022-12-28 23:47:41 -0500 (Wed, 28 Dec 2022) |
| EllapsedTime: 175.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: FastqCleaner.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:FastqCleaner.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings FastqCleaner_1.17.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/FastqCleaner.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 10.4.0
GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'FastqCleaner/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'FastqCleaner' version '1.17.0'
* package encoding: UTF-8
* 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 ... NOTE
Found the following non-portable file paths:
FastqCleaner/inst/application/www/help/docs/articles/Overview_files/figure-html/unnamed-chunk-11-1.png
FastqCleaner/inst/application/www/help/docs/articles/Overview_files/figure-html/unnamed-chunk-12-1.png
FastqCleaner/inst/application/www/help/docs/articles/Overview_files/figure-html/unnamed-chunk-13-1.png
FastqCleaner/inst/application/www/help/docs/articles/Overview_files/figure-html/unnamed-chunk-14-1.png
FastqCleaner/inst/application/www/help/docs/articles/Overview_files/figure-html/unnamed-chunk-7-1.png
FastqCleaner/inst/application/www/help/docs/articles/Overview_files/figure-html/unnamed-chunk-8-1.png
Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section 'Package structure' in the 'Writing R Extensions' manual.
* checking whether package 'FastqCleaner' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
* checking installed package size ... NOTE
installed size is 5.5Mb
sub-directories of 1Mb or more:
application 4.2Mb
libs 1.0Mb
* 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 ... 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 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-3.17-bioc/R/library/FastqCleaner/libs/x64/FastqCleaner.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 files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.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 NOTEs
See
'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/FastqCleaner.Rcheck/00check.log'
for details.
FastqCleaner.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL FastqCleaner ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'FastqCleaner' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 12.2.0' using C++11 g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cpp_GC_content.cpp -o cpp_GC_content.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cpp_base_content.cpp -o cpp_base_content.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cpp_check_quality_threshold.cpp -o cpp_check_quality_threshold.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cpp_create_stringvec.cpp -o cpp_create_stringvec.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cpp_which_true.cpp -o cpp_which_true.o g++ -shared -s -static-libgcc -o FastqCleaner.dll tmp.def RcppExports.o cpp_GC_content.o cpp_base_content.o cpp_check_quality_threshold.o cpp_create_stringvec.o cpp_which_true.o -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-FastqCleaner/00new/FastqCleaner/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 (FastqCleaner)
FastqCleaner.Rcheck/tests/testthat.Rout
R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
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.
> library(testthat)
> library(FastqCleaner)
>
> test_check("FastqCleaner")
[ FAIL 0 | WARN 0 | SKIP 10 | PASS 0 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• On CRAN (10)
[ FAIL 0 | WARN 0 | SKIP 10 | PASS 0 ]
>
> proc.time()
user system elapsed
6.60 0.60 7.18
FastqCleaner.Rcheck/FastqCleaner-Ex.timings
| name | user | system | elapsed | |
| adapter_filter | 0.23 | 0.05 | 0.28 | |
| check_encoding | 0.11 | 0.00 | 0.11 | |
| complex_filter | 0.23 | 0.02 | 0.25 | |
| fixed_filter | 0.22 | 0.01 | 0.23 | |
| inject_letter_random | 0.12 | 0.00 | 0.13 | |
| launch_fqc | 0 | 0 | 0 | |
| length_filter | 0.21 | 0.03 | 0.23 | |
| matching | 0.15 | 0.00 | 0.16 | |
| n_filter | 0.33 | 0.02 | 0.34 | |
| qmean_filter | 0.19 | 0.02 | 0.20 | |
| random_length | 0.03 | 0.00 | 0.03 | |
| random_qual | 0.01 | 0.00 | 0.02 | |
| random_seq | 0.02 | 0.00 | 0.01 | |
| seq_filter | 0.16 | 0.06 | 0.22 | |
| seq_names | 0.01 | 0.00 | 0.02 | |
| trim3q_filter | 0.27 | 0.03 | 0.29 | |
| unique_filter | 0.17 | 0.04 | 0.21 | |