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This page was generated on 2025-04-01 18:16 -0400 (Tue, 01 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 871 |
| 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 49/217 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | |||||||
| ChemmineR 3.59.0 (landing page) Thomas Girke
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | ERROR | ERROR | skipped | |||||||
|
To the developers/maintainers of the ChemmineR package: - 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: ChemmineR |
| Version: 3.59.0 |
| Command: /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL ChemmineR |
| StartedAt: 2025-04-01 18:05:59 -0400 (Tue, 01 Apr 2025) |
| EndedAt: 2025-04-01 18:06:01 -0400 (Tue, 01 Apr 2025) |
| EllapsedTime: 2.0 seconds |
| RetCode: 1 |
| Status: ERROR |
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### Running command:
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### /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL ChemmineR
###
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* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library’
* installing *source* package ‘ChemmineR’ ...
** this is package ‘ChemmineR’ version ‘3.59.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/BH/include' -I/usr/local/include -DNO_MAIN -DNO_DEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -fpic -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c DisjointSets.cpp -o DisjointSets.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/BH/include' -I/usr/local/include -DNO_MAIN -DNO_DEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -fpic -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c cluster.cc -o cluster.o
cluster.cc: In function ‘int nbr_intersect(std::vector<int>&, std::vector<int>&)’:
cluster.cc:118:18: 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:118:39: 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:131:24: 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:267:35: 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:284:28: 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:298:32: 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:314:28: 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:332:32: 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:390:28: 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)
| ^~~~~~~~~~~~~~~~~
cluster.cc:399:1: fatal error: error writing to /tmp/cckocFpL.s: No space left on device
399 | }
| ^
compilation terminated.
make: *** [/home/rapidbuild/bbs-3.21-bioc-rapid/R/etc/Makeconf:200: cluster.o] Error 1
ERROR: compilation failed for package ‘ChemmineR’
* removing ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/ChemmineR’
* restoring previous ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/ChemmineR’