Haakon Tjeldnes
| Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/ORFik |
| git_branch: RELEASE_3_17 |
| git_last_commit: 2536088 |
| git_last_commit_date: 2023-08-09 05:14:15 -0400 (Wed, 09 Aug 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:36:26 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 1445/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ORFik 1.20.2 (landing page) Haakon Tjeldnes
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the ORFik package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ORFik.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: ORFik |
| Version: 1.20.2 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL ORFik |
| StartedAt: 2023-10-15 16:29:57 -0400 (Sun, 15 Oct 2023) |
| EndedAt: 2023-10-15 16:32:00 -0400 (Sun, 15 Oct 2023) |
| EllapsedTime: 122.9 seconds |
| RetCode: 0 |
| Status: OK |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL ORFik
###
##############################################################################
##############################################################################
* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'ORFik' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
using C++11
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c findORFsHelpers.cpp -o findORFsHelpers.o
findORFsHelpers.cpp: In function 'Rcpp::IntegerMatrix orfs_as_matrix(std::string&, std::string, std::string, int)':
findORFsHelpers.cpp:214:21: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
214 | for (int i = 0; i < uorfSize/2; i++) {
| ~~^~~~~~~~~~~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c findOrfs.cpp -o findOrfs.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c findOrfsFasta.cpp -o findOrfsFasta.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pmapFromTranscripts.cpp -o pmapFromTranscripts.o
pmapFromTranscripts.cpp: In function 'Rcpp::List pmapFromTranscriptsCPP(const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const char&, bool)':
pmapFromTranscripts.cpp:151:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
151 | for(auto i = 0;i < xSize; i++){
| ~~^~~~~~~
pmapFromTranscripts.cpp:155:21: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
155 | for(auto i = 0; i < indexSize; i++){
| ~~^~~~~~~~~~~
pmapFromTranscripts.cpp:161:21: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
161 | for(auto i = 1; i < indexSize; i++){
| ~~^~~~~~~~~~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pmapToTranscripts.cpp -o pmapToTranscripts.o
pmapToTranscripts.cpp: In function 'void pmapToPositive(vi&, const int&, int&, const vi&, const vi&, const vi&, const vi&, const vi&, const vi&, const vi&, const vi&)':
pmapToTranscripts.cpp:22:7: warning: variable 'currentWidth' set but not used [-Wunused-but-set-variable]
22 | int currentWidth = 0;
| ^~~~~~~~~~~~
pmapToTranscripts.cpp: In function 'void pmapToNegative(vi&, const int&, int&, const vi&, const vi&, const vi&, const vi&, const vi&, const vi&, const vi&, const vi&)':
pmapToTranscripts.cpp:68:7: warning: variable 'currentWidth' set but not used [-Wunused-but-set-variable]
68 | int currentWidth = 0;
| ^~~~~~~~~~~~
pmapToTranscripts.cpp: In function 'Rcpp::List pmapToTranscriptsCPP(const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const char&, const std::vector<int>&)':
pmapToTranscripts.cpp:126:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
126 | for(auto i = 0;i < xSize; i++){ // Width per exon in x
| ~~^~~~~~~
pmapToTranscripts.cpp:130:21: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
130 | for(auto i = 0; i < indexSize; i++){ // Width per exon in tx
| ~~^~~~~~~~~~~
pmapToTranscripts.cpp:136:21: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
136 | for(auto i = 1; i < indexSize; i++){
| ~~^~~~~~~~~~~
pmapToTranscripts.cpp:147:22: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
147 | for (auto i = 1; i < 2 * xSize; i = i + 2) {
| ~~^~~~~~~~~~~
g++ -shared -s -static-libgcc -o ORFik.dll tmp.def RcppExports.o findORFsHelpers.o findOrfs.o findOrfsFasta.o pmapFromTranscripts.o pmapToTranscripts.o -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-ORFik/00new/ORFik/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'symbols' in package 'ORFik'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ORFik)