| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-11-20 12:02 -0500 (Wed, 20 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
| 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 908/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| groHMM 1.40.0 (landing page) Tulip Nandu
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | ERROR | skipped | ||||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | ERROR | skipped | ||||||||||
|
To the developers/maintainers of the groHMM package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/groHMM.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: groHMM |
| Version: 1.40.0 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL groHMM |
| StartedAt: 2024-11-19 15:59:15 -0500 (Tue, 19 Nov 2024) |
| EndedAt: 2024-11-19 15:59:44 -0500 (Tue, 19 Nov 2024) |
| EllapsedTime: 29.1 seconds |
| RetCode: 0 |
| Status: OK |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL groHMM
###
##############################################################################
##############################################################################
* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘groHMM’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c AnnotateProbes.c -o AnnotateProbes.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c DecayAlgorithm.c -o DecayAlgorithm.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c MLEfit.c -o MLEfit.o
In file included from MLEfit.c:43:
hmmHeader.h:301:16: warning: ‘expSum’ defined but not used [-Wunused-function]
301 | static double expSum(double *logValues, int length) {
| ^~~~~~
hmmHeader.h:281:16: warning: ‘MargainalizeSumLogProbOver’ defined but not used [-Wunused-function]
281 | static double MargainalizeSumLogProbOver(int state, int position,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c RegisterRRoutines.c -o RegisterRRoutines.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c Windowing.c -o Windowing.o
Windowing.c: In function ‘WindowAnalysis’:
Windowing.c:146:13: warning: unused variable ‘II’ [-Wunused-variable]
146 | int II = 0;
| ^~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c hmmEM.c -o hmmEM.o
In file included from hmmEM.c:50:
hmmHeader.h:301:16: warning: ‘expSum’ defined but not used [-Wunused-function]
301 | static double expSum(double *logValues, int length) {
| ^~~~~~
hmmHeader.h:281:16: warning: ‘MargainalizeSumLogProbOver’ defined but not used [-Wunused-function]
281 | static double MargainalizeSumLogProbOver(int state, int position,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from hmmHeader.h:36:
UsefulValues.h:39:15: warning: ‘VERY_LARGE_DOUBLE_VALUE’ defined but not used [-Wunused-variable]
39 | static double VERY_LARGE_DOUBLE_VALUE = 1e20;
| ^~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c hmmFwBw.c -o hmmFwBw.o
hmmFwBw.c: In function ‘forward’:
hmmFwBw.c:142:7: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
142 | for(k=1; k<n; k++)
| ^~~
hmmFwBw.c:145:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
145 | for (k = 0; k<n; k++) {
| ^~~
In file included from hmmFwBw.c:45:
hmmHeader.h: At top level:
hmmHeader.h:301:16: warning: ‘expSum’ defined but not used [-Wunused-function]
301 | static double expSum(double *logValues, int length) {
| ^~~~~~
hmmHeader.h:281:16: warning: ‘MargainalizeSumLogProbOver’ defined but not used [-Wunused-function]
281 | static double MargainalizeSumLogProbOver(int state, int position,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from hmmHeader.h:36:
UsefulValues.h:39:15: warning: ‘VERY_LARGE_DOUBLE_VALUE’ defined but not used [-Wunused-variable]
39 | static double VERY_LARGE_DOUBLE_VALUE = 1e20;
| ^~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c hmmMiscFunctions.c -o hmmMiscFunctions.o
hmmMiscFunctions.c: In function ‘SStatsGamma’:
hmmMiscFunctions.c:235:37: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘double’ [-Wformat=]
235 | if(!(logPP <= epsilon)) Rprintf("[SSallocGamma] -- \
| ^~~~~~~~~~~~~~~~~~~~
236 | Assertion about to fail! logPP= %d\n", logPP);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~
| |
| double
hmmMiscFunctions.c: In function ‘SStatsNormExp’:
hmmMiscFunctions.c:384:10: warning: unused variable ‘wi’ [-Wunused-variable]
384 | double wi, *newEx;
| ^~
hmmMiscFunctions.c: In function ‘UpdateNormExp’:
hmmMiscFunctions.c:417:10: warning: unused variable ‘epsilon’ [-Wunused-variable]
417 | double epsilon=0.00001;
| ^~~~~~~
In file included from hmmHeader.h:36,
from hmmMiscFunctions.c:43:
UsefulValues.h: At top level:
UsefulValues.h:39:15: warning: ‘VERY_LARGE_DOUBLE_VALUE’ defined but not used [-Wunused-variable]
39 | static double VERY_LARGE_DOUBLE_VALUE = 1e20;
| ^~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c hmmViterbi.c -o hmmViterbi.o
In file included from hmmViterbi.c:48:
hmmHeader.h:301:16: warning: ‘expSum’ defined but not used [-Wunused-function]
301 | static double expSum(double *logValues, int length) {
| ^~~~~~
hmmHeader.h:281:16: warning: ‘MargainalizeSumLogProbOver’ defined but not used [-Wunused-function]
281 | static double MargainalizeSumLogProbOver(int state, int position,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from hmmHeader.h:36:
UsefulValues.h:39:15: warning: ‘VERY_LARGE_DOUBLE_VALUE’ defined but not used [-Wunused-variable]
39 | static double VERY_LARGE_DOUBLE_VALUE = 1e20;
| ^~~~~~~~~~~~~~~~~~~~~~~
gcc -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o groHMM.so AnnotateProbes.o DecayAlgorithm.o MLEfit.o RegisterRRoutines.o Windowing.o hmmEM.o hmmFwBw.o hmmMiscFunctions.o hmmViterbi.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-groHMM/00new/groHMM/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 (groHMM)