August Guang
| Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/qckitfastq |
| git_branch: devel |
| git_last_commit: 6d6381d |
| git_last_commit_date: 2024-10-29 10:35:25 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-24 11:47 -0500 (Tue, 24 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
| 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 1613/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| qckitfastq 1.23.0 (landing page) August Guang
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
To the developers/maintainers of the qckitfastq package: - 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 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: qckitfastq |
| Version: 1.23.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:qckitfastq.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings qckitfastq_1.23.0.tar.gz |
| StartedAt: 2024-12-24 10:04:51 -0000 (Tue, 24 Dec 2024) |
| EndedAt: 2024-12-24 10:06:08 -0000 (Tue, 24 Dec 2024) |
| EllapsedTime: 77.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: qckitfastq.Rcheck |
| Warnings: 1 |
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### Running command:
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### /home/biocbuild/R/R/bin/R CMD check --install=check:qckitfastq.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings qckitfastq_1.23.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/qckitfastq.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘qckitfastq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘qckitfastq’ version ‘1.23.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘qckitfastq’ can be installed ... WARNING
Found the following significant warnings:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RSeqAn/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RSeqAn/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RSeqAn/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RSeqAn/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RSeqAn/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RSeqAn/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RSeqAn/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RSeqAn/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RSeqAn/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RSeqAn/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RSeqAn/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RSeqAn/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RSeqAn/include/seqan/file/string_external.h:1338:41: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RSeqAn/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RSeqAn/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
See ‘/home/biocbuild/bbs-3.21-bioc/meat/qckitfastq.Rcheck/00install.out’ for details.
* used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* checking C++ specification ... NOTE
Specified C++14: please drop specification unless essential
* 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 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 loading without being on the library search path ... 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
run_all 14.125 0.163 14.321
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.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, 2 NOTEs
See
‘/home/biocbuild/bbs-3.21-bioc/meat/qckitfastq.Rcheck/00check.log’
for details.
qckitfastq.Rcheck/00install.out
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### Running command:
###
### /home/biocbuild/R/R/bin/R CMD INSTALL qckitfastq
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘qckitfastq’ ...
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
using C++14
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RSeqAn/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RSeqAn/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c calc_adapter_content.cpp -o calc_adapter_content.o
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RSeqAn/include/seqan/modifier.h:74,
from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RSeqAn/include/seqan/find.h:44,
from calc_adapter_content.cpp:7:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RSeqAn/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
79 | struct FunctorUpcase : public std::unary_function<InType, Result>
| ^~~~~~~~~~~~~~
In file included from /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/string:49,
from /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/locale_classes.h:40,
from /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/ios_base.h:41,
from /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/ios:44,
from /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/ostream:40,
from /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/iostream:41,
from calc_adapter_content.cpp:1:
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RSeqAn/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
113 | struct FunctorLowcase : public std::unary_function<InType, Result>
| ^~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RSeqAn/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
147 | struct FunctorConvert : public std::unary_function<InType,OutType>
| ^~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RSeqAn/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
219 | struct FunctorComplement<char> : public std::unary_function<Dna5,Dna5>
| ^~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RSeqAn/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
228 | struct FunctorComplement<Dna> : public std::unary_function<Dna,Dna>
| ^~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RSeqAn/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
237 | struct FunctorComplement<Dna5> : public std::unary_function<Dna5,Dna5>
| ^~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RSeqAn/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
246 | struct FunctorComplement<Rna> : public std::unary_function<Rna,Rna>
| ^~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RSeqAn/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
255 | struct FunctorComplement<Rna5> : public std::unary_function<Rna5,Rna5>
| ^~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RSeqAn/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
264 | struct FunctorComplement<DnaQ> : public std::unary_function<DnaQ,DnaQ>
| ^~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RSeqAn/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
276 | struct FunctorComplement<Dna5Q> : public std::unary_function<Dna5Q,Dna5Q>
| ^~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RSeqAn/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
287 | struct FunctorComplement<Iupac> : public std::unary_function<Iupac,Iupac>
| ^~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RSeqAn/include/seqan/modifier.h:79:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RSeqAn/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
393 | struct PosLess_ : public std::binary_function<TPos, TPos, bool>
| ^~~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RSeqAn/include/seqan/file.h:101,
from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RSeqAn/include/seqan/stream.h:62,
from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RSeqAn/include/seqan/score.h:43,
from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RSeqAn/include/seqan/find.h:45:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RSeqAn/include/seqan/file/string_external.h:1338:41: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
1338 | struct testIODone : public std::unary_function<TPageFrame&,bool>
| ^~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RSeqAn/include/seqan/graph_algorithms.h:48,
from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RSeqAn/include/seqan/find.h:47:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RSeqAn/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
325 | public std::unary_function<Pair<TKey, TValue>, bool>
| ^~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RSeqAn/include/seqan/graph_algorithms.h:62:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RSeqAn/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
63 | struct LessPairI1_ : public std::unary_function<Pair<TWeight, TPair>, bool>
| ^~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RSeqAn/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c gzstream.cpp -o gzstream.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RSeqAn/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -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 unsigned int’} [-Wsign-compare]
181 | if (pos_counter <= qual_score_matrix.size()) {
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o qckitfastq.so RcppExports.o calc_adapter_content.o gzstream.o read_fastq.o -lz -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-qckitfastq/00new/qckitfastq/libs
** 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
** 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 (qckitfastq)
qckitfastq.Rcheck/tests/testthat.Rout
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Platform: aarch64-unknown-linux-gnu
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> library(testthat)
> library(qckitfastq)
>
> test_check("qckitfastq")
[fastqq] File ( 1/1) '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/qckitfastq/extdata/10^5_reads_test.fq.gz' done.
[fastq_Klocs] File ( 1/1) '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/qckitfastq/extdata/10^5_reads_test.fq.gz' done.
[fastqq] File ( 1/1) '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/qckitfastq/extdata/10^5_reads_test.fq.gz' done.
[fastqq] File ( 1/1) '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/qckitfastq/extdata/10^5_reads_test.fq.gz' done.
[fastq_Klocs] File ( 1/1) '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/qckitfastq/extdata/10^5_reads_test.fq.gz' done.
[fastqq] File ( 1/1) '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/qckitfastq/extdata/10^5_reads_test.fq.gz' done.
[fastq_Klocs] File ( 1/1) '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/qckitfastq/extdata/10^5_reads_test.fq.gz' done.
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 37 ]
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 37 ]
>
> proc.time()
user system elapsed
22.157 0.348 22.561
qckitfastq.Rcheck/qckitfastq-Ex.timings
| name | user | system | elapsed | |
| GC_content | 0.047 | 0.008 | 0.057 | |
| adapter_content | 0.000 | 0.004 | 0.006 | |
| calc_adapter_content | 0.003 | 0.000 | 0.003 | |
| calc_format_score | 0 | 0 | 0 | |
| calc_over_rep_seq | 0.046 | 0.004 | 0.049 | |
| dimensions | 0.127 | 0.004 | 0.131 | |
| find_format | 0.001 | 0.000 | 0.001 | |
| gc_per_read | 0.049 | 0.000 | 0.050 | |
| kmer_count | 0.062 | 0.000 | 0.062 | |
| overrep_kmer | 0.377 | 0.032 | 0.409 | |
| overrep_reads | 0.049 | 0.004 | 0.053 | |
| per_base_quality | 0.176 | 0.004 | 0.180 | |
| per_read_quality | 0.175 | 0.000 | 0.175 | |
| plot_GC_content | 0.521 | 0.004 | 0.527 | |
| plot_adapter_content | 0.229 | 0.016 | 0.245 | |
| plot_overrep_kmer | 0.667 | 0.012 | 0.680 | |
| plot_overrep_reads | 0.225 | 0.000 | 0.225 | |
| plot_per_base_quality | 1.459 | 0.000 | 1.462 | |
| plot_per_read_quality | 0.350 | 0.004 | 0.355 | |
| plot_read_content | 0.373 | 0.028 | 0.402 | |
| plot_read_length | 0.264 | 0.000 | 0.263 | |
| qual_score_per_read | 0.173 | 0.004 | 0.177 | |
| read_base_content | 0.069 | 0.004 | 0.074 | |
| read_content | 0.077 | 0.000 | 0.077 | |
| read_length | 0.003 | 0.000 | 0.003 | |
| run_all | 14.125 | 0.163 | 14.321 | |