August Guang
| Snapshot Date: 2025-01-02 13:00 -0500 (Thu, 02 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/qckitfastq |
| git_branch: RELEASE_3_20 |
| git_last_commit: c770a15 |
| git_last_commit_date: 2024-10-29 10:35:25 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-01-09 12:11 -0500 (Thu, 09 Jan 2025).
| 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 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4358 |
| 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 1624/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| qckitfastq 1.22.0 (landing page) August Guang
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
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: 1.22.0 |
| Command: /home/biocbuild/R/R/bin/R CMD INSTALL qckitfastq |
| StartedAt: 2025-01-08 20:02:01 -0000 (Wed, 08 Jan 2025) |
| EndedAt: 2025-01-08 20:02:25 -0000 (Wed, 08 Jan 2025) |
| EllapsedTime: 23.7 seconds |
| RetCode: 0 |
| Status: OK |
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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-4.4.2/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-4.4.2/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.2/site-library/RSeqAn/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -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-4.4.2/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.2/site-library/RSeqAn/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c calc_adapter_content.cpp -o calc_adapter_content.o
In file included from /home/biocbuild/R/R-4.4.2/site-library/RSeqAn/include/seqan/modifier.h:74,
from /home/biocbuild/R/R-4.4.2/site-library/RSeqAn/include/seqan/find.h:44,
from calc_adapter_content.cpp:7:
/home/biocbuild/R/R-4.4.2/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-4.4.2/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-4.4.2/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-4.4.2/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-4.4.2/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-4.4.2/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-4.4.2/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-4.4.2/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-4.4.2/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-4.4.2/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-4.4.2/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-4.4.2/site-library/RSeqAn/include/seqan/modifier.h:79:
/home/biocbuild/R/R-4.4.2/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-4.4.2/site-library/RSeqAn/include/seqan/file.h:101,
from /home/biocbuild/R/R-4.4.2/site-library/RSeqAn/include/seqan/stream.h:62,
from /home/biocbuild/R/R-4.4.2/site-library/RSeqAn/include/seqan/score.h:43,
from /home/biocbuild/R/R-4.4.2/site-library/RSeqAn/include/seqan/find.h:45:
/home/biocbuild/R/R-4.4.2/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-4.4.2/site-library/RSeqAn/include/seqan/graph_algorithms.h:48,
from /home/biocbuild/R/R-4.4.2/site-library/RSeqAn/include/seqan/find.h:47:
/home/biocbuild/R/R-4.4.2/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-4.4.2/site-library/RSeqAn/include/seqan/graph_algorithms.h:62:
/home/biocbuild/R/R-4.4.2/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-4.4.2/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.2/site-library/RSeqAn/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -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-4.4.2/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.2/site-library/RSeqAn/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -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-4.4.2/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)