| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-24 11:40 -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 1384/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| NanoMethViz 3.3.1 (landing page) Shian Su
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | ERROR | ERROR | skipped | |||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | ERROR | ERROR | skipped | skipped | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | ERROR | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | ERROR | ERROR | skipped | skipped | |||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
|
To the developers/maintainers of the NanoMethViz package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/NanoMethViz.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: NanoMethViz |
| Version: 3.3.1 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL NanoMethViz |
| StartedAt: 2024-12-23 15:44:50 -0500 (Mon, 23 Dec 2024) |
| EndedAt: 2024-12-23 15:45:16 -0500 (Mon, 23 Dec 2024) |
| EllapsedTime: 25.7 seconds |
| RetCode: 1 |
| Status: ERROR |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL NanoMethViz
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘NanoMethViz’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++20
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c convert_methy_to_dss.cpp -o convert_methy_to_dss.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c count_cg.cpp -o count_cg.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c genome.cpp -o genome.o
genome.cpp: In member function ‘bool Genome::check_if_motif(const std::string&, int, const std::string&, int)’:
genome.cpp:43:21: warning: variable ‘chrom_view’ set but not used [-Wunused-but-set-variable]
43 | string_view chrom_view = this->bases_at(chrom, motif_start, motif_end);
| ^~~~~~~~~~
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c modbam.cpp -o modbam.o
modbam.cpp: In function ‘GenomicModPos parse_bam(const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, int)’:
modbam.cpp:331:44: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::basic_string_view<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
331 | while ( mod_string_end < mm_tok.size() && std::isalnum(mm_tok[mod_string_end]) ) {
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
modbam.cpp:339:40: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::basic_string_view<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
339 | if (mod_string_end == mm_tok.size() || mm_tok[mod_string_end] == '?') {
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
modbam.cpp:363:17: warning: ‘target_base’ may be used uninitialized [-Wmaybe-uninitialized]
363 | if (seq.at(seq_ind) == target_base) {
| ^~
modbam.cpp:305:14: note: ‘target_base’ was declared here
305 | char target_base;
| ^~~~~~~~~~~
modbam.cpp:364:21: warning: ‘parse_mode’ may be used uninitialized [-Wmaybe-uninitialized]
364 | switch (parse_mode) {
| ^~~~~~
modbam.cpp:308:19: note: ‘parse_mode’ was declared here
308 | ParseMode parse_mode;
| ^~~~~~~~~~
In file included from /usr/include/c++/13/bits/stl_iterator.h:85,
from /usr/include/c++/13/bits/stl_algobase.h:67,
from /usr/include/c++/13/algorithm:60,
from modbam.cpp:1:
In function ‘constexpr decltype (::new(void*(0)) _Tp) std::construct_at(_Tp*, _Args&& ...) [with _Tp = char; _Args = {const char&}]’,
inlined from ‘static constexpr void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = char; _Args = {const char&}; _Tp = char]’ at /usr/include/c++/13/bits/alloc_traits.h:540:21,
inlined from ‘constexpr void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const char&}; _Tp = char; _Alloc = std::allocator<char>]’ at /usr/include/c++/13/bits/vector.tcc:468:28,
inlined from ‘constexpr void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = char; _Alloc = std::allocator<char>]’ at /usr/include/c++/13/bits/stl_vector.h:1292:21,
inlined from ‘GenomicModPos parse_bam(const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, int)’ at modbam.cpp:368:50:
/usr/include/c++/13/bits/stl_construct.h:97:14: warning: ‘current_base’ may be used uninitialized [-Wmaybe-uninitialized]
97 | { return ::new((void*)__location) _Tp(std::forward<_Args>(__args)...); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
modbam.cpp: In function ‘GenomicModPos parse_bam(const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, int)’:
modbam.cpp:304:14: note: ‘current_base’ was declared here
304 | char current_base;
| ^~~~~~~~~~~~
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c utils.cpp -o utils.o
g++ -std=gnu++20 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o NanoMethViz.so RcppExports.o convert_methy_to_dss.o count_cg.o genome.o modbam.o utils.o -lz -hts -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
g++: error: unrecognized command-line option ‘-h’
make: *** [/home/biocbuild/bbs-3.21-bioc/R/share/make/shlib.mk:10: NanoMethViz.so] Error 1
ERROR: compilation failed for package ‘NanoMethViz’
* removing ‘/home/biocbuild/bbs-3.21-bioc/R/site-library/NanoMethViz’
* restoring previous ‘/home/biocbuild/bbs-3.21-bioc/R/site-library/NanoMethViz’