August Guang
| Snapshot Date: 2022-08-17 14:00:04 -0400 (Wed, 17 Aug 2022) |
| git_url: https://git.bioconductor.org/packages/qckitfastq |
| git_branch: master |
| git_last_commit: 4e7f31a |
| git_last_commit_date: 2022-04-26 11:53:43 -0400 (Tue, 26 Apr 2022) |
| Back to Multiple platform build/check report for BioC 3.16 |
|
This page was generated on 2022-08-18 11:07:03 -0400 (Thu, 18 Aug 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4379 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4161 |
| lconway | macOS 12.2.1 Monterey | x86_64 | 4.2.1 Patched (2022-07-09 r82577) -- "Funny-Looking Kid" | 4169 |
| 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 qckitfastq package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/qckitfastq.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 1529/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| qckitfastq 1.13.0 (landing page) August Guang
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.2.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: qckitfastq |
| Version: 1.13.0 |
| Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:qckitfastq.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings qckitfastq_1.13.0.tar.gz |
| StartedAt: 2022-08-18 04:50:59 -0400 (Thu, 18 Aug 2022) |
| EndedAt: 2022-08-18 04:52:39 -0400 (Thu, 18 Aug 2022) |
| EllapsedTime: 99.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: qckitfastq.Rcheck |
| Warnings: 0 |
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### Running command:
###
### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:qckitfastq.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings qckitfastq_1.13.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/qckitfastq.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 'qckitfastq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'qckitfastq' version '1.13.0'
* 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 ... OK
* checking whether package 'qckitfastq' can be installed ... OK
* 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 ... 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-3.16-bioc/R/library/qckitfastq/libs/x64/qckitfastq.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. 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
run_all 10.74 2.25 13.08
* 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: 1 NOTE
See
'F:/biocbuild/bbs-3.16-bioc/meat/qckitfastq.Rcheck/00check.log'
for details.
qckitfastq.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.16/bioc/src/contrib/qckitfastq_1.13.0.tar.gz && rm -rf qckitfastq.buildbin-libdir && mkdir qckitfastq.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=qckitfastq.buildbin-libdir qckitfastq_1.13.0.tar.gz && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL qckitfastq_1.13.0.zip && rm qckitfastq_1.13.0.tar.gz qckitfastq_1.13.0.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 747k 100 747k 0 0 2981k 0 --:--:-- --:--:-- --:--:-- 2989k
only one architecture so ignoring '--merge-multiarch'
* installing *source* package 'qckitfastq' ...
** using staged installation
** libs
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RSeqAn/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-3.16-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RSeqAn/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c calc_adapter_content.cpp -o calc_adapter_content.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RSeqAn/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c gzstream.cpp -o gzstream.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include" -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RSeqAn/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c read_fastq.cpp -o read_fastq.o
read_fastq.cpp: In function 'Rcpp::List qual_score_per_read(std::string)':
read_fastq.cpp:181:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::map<int, std::vector<unsigned char> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
181 | if (pos_counter <= qual_score_matrix.size()) {
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -shared -s -static-libgcc -o qckitfastq.dll tmp.def RcppExports.o calc_adapter_content.o gzstream.o read_fastq.o -LF:/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -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/qckitfastq.buildbin-libdir/00LOCK-qckitfastq/00new/qckitfastq/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
* MD5 sums
packaged installation of 'qckitfastq' as qckitfastq_1.13.0.zip
* DONE (qckitfastq)
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
package 'qckitfastq' successfully unpacked and MD5 sums checked
qckitfastq.Rcheck/tests/testthat.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.
> library(testthat)
> library(qckitfastq)
>
> test_check("qckitfastq")
[fastqq] File ( 1/1) 'F:/biocbuild/bbs-3.16-bioc/R/library/qckitfastq/extdata/10^5_reads_test.fq.gz' done.
[fastq_Klocs] File ( 1/1) 'F:/biocbuild/bbs-3.16-bioc/R/library/qckitfastq/extdata/10^5_reads_test.fq.gz' done.
[fastqq] File ( 1/1) 'F:/biocbuild/bbs-3.16-bioc/R/library/qckitfastq/extdata/10^5_reads_test.fq.gz' done.
[fastqq] File ( 1/1) 'F:/biocbuild/bbs-3.16-bioc/R/library/qckitfastq/extdata/10^5_reads_test.fq.gz' done.
[fastq_Klocs] File ( 1/1) 'F:/biocbuild/bbs-3.16-bioc/R/library/qckitfastq/extdata/10^5_reads_test.fq.gz' done.
[fastqq] File ( 1/1) 'F:/biocbuild/bbs-3.16-bioc/R/library/qckitfastq/extdata/10^5_reads_test.fq.gz' done.
[fastq_Klocs] File ( 1/1) 'F:/biocbuild/bbs-3.16-bioc/R/library/qckitfastq/extdata/10^5_reads_test.fq.gz' done.
[1] "adapter_content not available for Windows; skipping"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 27 ]
>
> proc.time()
user system elapsed
17.34 2.85 20.18
qckitfastq.Rcheck/qckitfastq-Ex.timings
| name | user | system | elapsed | |
| GC_content | 0.11 | 0.00 | 0.12 | |
| adapter_content | 0 | 0 | 0 | |
| calc_adapter_content | 0 | 0 | 0 | |
| calc_format_score | 0 | 0 | 0 | |
| calc_over_rep_seq | 0.06 | 0.00 | 0.06 | |
| dimensions | 0.14 | 0.01 | 0.15 | |
| find_format | 0 | 0 | 0 | |
| gc_per_read | 0.1 | 0.0 | 0.1 | |
| kmer_count | 0.04 | 0.00 | 0.04 | |
| overrep_kmer | 0.28 | 0.02 | 0.30 | |
| overrep_reads | 0.05 | 0.00 | 0.05 | |
| per_base_quality | 0.17 | 0.00 | 0.17 | |
| per_read_quality | 0.17 | 0.00 | 0.17 | |
| plot_GC_content | 0.46 | 0.05 | 0.50 | |
| plot_adapter_content | 0 | 0 | 0 | |
| plot_overrep_kmer | 0.47 | 0.01 | 0.49 | |
| plot_overrep_reads | 0.18 | 0.00 | 0.18 | |
| plot_per_base_quality | 0.93 | 0.03 | 0.96 | |
| plot_per_read_quality | 0.31 | 0.00 | 0.31 | |
| plot_read_content | 0.29 | 0.00 | 0.30 | |
| plot_read_length | 0.25 | 0.00 | 0.25 | |
| qual_score_per_read | 0.18 | 0.00 | 0.17 | |
| read_base_content | 0.06 | 0.00 | 0.06 | |
| read_content | 0.06 | 0.00 | 0.06 | |
| read_length | 0 | 0 | 0 | |
| run_all | 10.74 | 2.25 | 13.08 | |