Tulip Nandu
| Snapshot Date: 2026-04-17 13:40 -0400 (Fri, 17 Apr 2026) |
| git_url: https://git.bioconductor.org/packages/groHMM |
| git_branch: devel |
| git_last_commit: a2e7235 |
| git_last_commit_date: 2025-10-29 10:22:30 -0400 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-18 11:37 -0400 (Sat, 18 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 alpha (2026-04-05 r89794) | 4957 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-04-08 r89818) | 4686 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4627 |
| 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 946/2404 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| groHMM 1.45.0 (landing page) Tulip Nandu
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | ERROR | ERROR | skipped | ||||||||||
| See other builds for groHMM in R Universe. | ||||||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: groHMM |
| Version: 1.45.0 |
| Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data groHMM |
| StartedAt: 2026-04-16 23:59:47 -0000 (Thu, 16 Apr 2026) |
| EndedAt: 2026-04-17 00:00:01 -0000 (Fri, 17 Apr 2026) |
| EllapsedTime: 14.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data groHMM
###
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* checking for file ‘groHMM/DESCRIPTION’ ... OK
* preparing ‘groHMM’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
-----------------------------------
* installing *source* package ‘groHMM’ ...
** this is package ‘groHMM’ version ‘1.45.0’
** using staged installation
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c AnnotateProbes.c -o AnnotateProbes.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c DecayAlgorithm.c -o DecayAlgorithm.o
DecayAlgorithm.c: In function ‘getTranscriptPositions’:
DecayAlgorithm.c:94:15: warning: unused variable ‘false_value’ [-Wunused-variable]
94 | const int false_value= 0;
| ^~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -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,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c RegisterRRoutines.c -o RegisterRRoutines.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -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;
| ^~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -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;
| ^~~~~~~~~~~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -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;
| ^~~~~~~~~~~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -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;
| ^~~~~~~~~~~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -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;
| ^~~~~~~~~~~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -shared -L/home/biocbuild/R/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/R/R/lib -lR
installing to /home/biocbuild/tmp/Rtmpv9zgtC/Rinsta6ca938b1811a/00LOCK-groHMM/00new/groHMM/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Error: package or namespace load failed for ‘Rsamtools’:
class "Seqinfo" is not exported by 'namespace:GenomeInfoDb'
Execution halted
ERROR: lazy loading failed for package ‘groHMM’
* removing ‘/home/biocbuild/tmp/Rtmpv9zgtC/Rinsta6ca938b1811a/groHMM’
-----------------------------------
ERROR: package installation failed