Thomas Girke
| Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/ChemmineR |
| git_branch: devel |
| git_last_commit: e47622d |
| git_last_commit_date: 2023-11-07 14:23:22 -0400 (Tue, 07 Nov 2023) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:40:25 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| 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 326/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ChemmineR 3.55.1 (landing page) Thomas Girke
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
To the developers/maintainers of the ChemmineR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ChemmineR.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: ChemmineR |
| Version: 3.55.1 |
| Command: /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL ChemmineR |
| StartedAt: 2024-03-27 20:27:00 -0000 (Wed, 27 Mar 2024) |
| EndedAt: 2024-03-27 20:27:44 -0000 (Wed, 27 Mar 2024) |
| EllapsedTime: 43.5 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL ChemmineR
###
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* installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library’
* installing *source* package ‘ChemmineR’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include' -I/usr/local/include -DNO_MAIN -DNO_DEBUG -fPIC -g -O2 -Wall -c DisjointSets.cpp -o DisjointSets.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include' -I/usr/local/include -DNO_MAIN -DNO_DEBUG -fPIC -g -O2 -Wall -c cluster.cc -o cluster.o
cluster.cc: In function ‘int nbr_intersect(std::vector<int>&, std::vector<int>&)’:
cluster.cc:118:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
118 | while (i < nbrs1.size() and j < nbrs2.size()) {
| ~~^~~~~~~~~~~~~~
cluster.cc:118:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
118 | while (i < nbrs1.size() and j < nbrs2.size()) {
| ~~^~~~~~~~~~~~~~
cluster.cc: In function ‘int contains(int, std::vector<int>&)’:
cluster.cc:131:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
131 | for(int i=0; i < list.size(); i++)
| ~~^~~~~~~~~~~~~
cluster.cc: In function ‘DisjointSets cluster(int, int, int, int)’:
cluster.cc:267:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
267 | for (int j = 0; j < nbr_list[i].size(); j ++) {
| ~~^~~~~~~~~~~~~~~~~~~~
cluster.cc: In function ‘void loadNNMatrix(int, int, int, SEXP)’:
cluster.cc:284:21: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
284 | for(unsigned i=0; i<N; i++) //rows
| ~^~
cluster.cc:298:18: warning: comparison of integer expressions of different signedness: ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
298 | if(nbrs.size() < minNbrs) // will end up a singleton
| ~~~~~~~~~~~~^~~~~~~~~
cluster.cc: In function ‘void loadNNList(int, int, SEXP)’:
cluster.cc:314:21: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
314 | for(unsigned i=0; i<N; i++) //rows
| ~^~
cluster.cc:332:18: warning: comparison of integer expressions of different signedness: ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
332 | if(nbrs.size() < minNbrs) // will end up a singleton
| ~~~~~~~~~~~~^~~~~~~~~
cluster.cc: In function ‘SEXPREC* jarvis_patrick(SEXP, SEXP, SEXP, SEXP, SEXP)’:
cluster.cc:390:21: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
390 | for(unsigned i=0; i<N; i++){
| ~^~
cluster.cc: At global scope:
cluster.cc:49:13: warning: ‘void prepare_neighbors(const char*, int, int)’ defined but not used [-Wunused-function]
49 | void static prepare_neighbors(const char* nbr_file, int skip, int p)
| ^~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include' -I/usr/local/include -DNO_MAIN -DNO_DEBUG -fPIC -g -O2 -Wall -c cstrsplit.cc -o cstrsplit.o
In file included from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/range/as_literal.hpp:18,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/algorithm/string/trim.hpp:19,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/algorithm/string.hpp:19,
from cstrsplit.cc:7:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
In file included from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/bind/mem_fn.hpp:25,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/mem_fn.hpp:22,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/function/detail/prologue.hpp:19,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/function.hpp:30,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/algorithm/string/iter_find.hpp:27,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/algorithm/string/split.hpp:16,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/algorithm/string.hpp:23,
from cstrsplit.cc:7:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include/Rcpp.h:27,
from cstrsplit.cc:2:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include' -I/usr/local/include -DNO_MAIN -DNO_DEBUG -fPIC -g -O2 -Wall -c desc.cc -o desc.o
desc.cc: In function ‘SEXPREC* genAPDescriptor(SEXP)’:
desc.cc:249:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<unsigned int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
249 | for(int i=0; i < descs.size(); i++)
| ~~^~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include' -I/usr/local/include -DNO_MAIN -DNO_DEBUG -fPIC -g -O2 -Wall -c fingerprints.cc -o fingerprints.o
fingerprints.cc: In function ‘SEXPREC* uniquifyAtomPairs(SEXP)’:
fingerprints.cc:138:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IndexedValue*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
138 | for(int i=0; i < aps.size(); i++)
| ~~^~~~~~~~~~~~
fingerprints.cc:145:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IndexedValue*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
145 | for(int i=0; i < aps.size(); i++){
| ~~^~~~~~~~~~~~
fingerprints.cc:158:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<IndexedValue*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
158 | for(int i=0; i < aps.size(); i++){
| ~~^~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include' -I/usr/local/include -DNO_MAIN -DNO_DEBUG -fPIC -g -O2 -Wall -c formats.cc -o formats.o
formats.cc: In function ‘int sdf_iter(std::fstream&, std::string&, int&)’:
formats.cc:237:10: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying 4 bytes from a string of length 100001 [-Wstringop-truncation]
237 | strncpy(buf_4, line, 4);
| ~~~~~~~^~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include' -I/usr/local/include -DNO_MAIN -DNO_DEBUG -fPIC -g -O2 -Wall -c molecule.cc -o molecule.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include' -I/usr/local/include -DNO_MAIN -DNO_DEBUG -fPIC -g -O2 -Wall -c r_wrap.cc -o r_wrap.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include' -I/usr/local/include -DNO_MAIN -DNO_DEBUG -fPIC -g -O2 -Wall -c script.cc -o script.o
In file included from script.cc:2:
desc.h:39:13: warning: ‘elements’ defined but not used [-Wunused-variable]
39 | static char elements[112][3] = {
| ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include' -I/usr/local/include -DNO_MAIN -DNO_DEBUG -fPIC -g -O2 -Wall -c similarity.cc -o similarity.o
In file included from similarity.cc:1:
desc.h:39:13: warning: ‘elements’ defined but not used [-Wunused-variable]
39 | static char elements[112][3] = {
| ^~~~~~~~
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -L/usr/local/lib -o ChemmineR.so DisjointSets.o cluster.o cstrsplit.o desc.o fingerprints.o formats.o molecule.o r_wrap.o script.o similarity.o -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -lR
installing to /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/00LOCK-ChemmineR/00new/ChemmineR/libs
** R
** data
** 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 (ChemmineR)