Tulip Nandu
| Snapshot Date: 2025-01-03 13:40 -0500 (Fri, 03 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/groHMM |
| git_branch: devel |
| git_last_commit: 8d0b05a |
| git_last_commit_date: 2024-12-03 18:09:10 -0500 (Tue, 03 Dec 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-04 11:45 -0500 (Sat, 04 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4756 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4475 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4435 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4390 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4383 |
| 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 903/2275 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| groHMM 1.41.0 (landing page) Tulip Nandu
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | ERROR | ERROR | skipped | |||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | ERROR | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | ERROR | ERROR | skipped | skipped | |||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | ERROR | 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: 1.41.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data groHMM |
| StartedAt: 2025-01-03 16:35:12 -0500 (Fri, 03 Jan 2025) |
| EndedAt: 2025-01-03 16:35:13 -0500 (Fri, 03 Jan 2025) |
| EllapsedTime: 1.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
###
### /Library/Frameworks/R.framework/Resources/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’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c AnnotateProbes.c -o AnnotateProbes.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c DecayAlgorithm.c -o DecayAlgorithm.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c MLEfit.c -o MLEfit.o
MLEfit.c:260:25: warning: variable 'cnt' set but not used [-Wunused-but-set-variable]
int maxn = 2*n_x+1, cnt=0;
^
In file included from MLEfit.c:43:
./hmmHeader.h:281:16: warning: unused function 'MargainalizeSumLogProbOver' [-Wunused-function]
static double MargainalizeSumLogProbOver(int state, int position,
^
./hmmHeader.h:301:16: warning: unused function 'expSum' [-Wunused-function]
static double expSum(double *logValues, int length) {
^
3 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RegisterRRoutines.c -o RegisterRRoutines.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Windowing.c -o Windowing.o
Windowing.c:146:6: warning: unused variable 'II' [-Wunused-variable]
int II = 0;
^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c hmmEM.c -o hmmEM.o
In file included from hmmEM.c:50:
./hmmHeader.h:281:16: warning: unused function 'MargainalizeSumLogProbOver' [-Wunused-function]
static double MargainalizeSumLogProbOver(int state, int position,
^
./hmmHeader.h:301:16: warning: unused function 'expSum' [-Wunused-function]
static double expSum(double *logValues, int length) {
^
2 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c hmmFwBw.c -o hmmFwBw.o
In file included from hmmFwBw.c:45:
./hmmHeader.h:281:16: warning: unused function 'MargainalizeSumLogProbOver' [-Wunused-function]
static double MargainalizeSumLogProbOver(int state, int position,
^
./hmmHeader.h:301:16: warning: unused function 'expSum' [-Wunused-function]
static double expSum(double *logValues, int length) {
^
2 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c hmmMiscFunctions.c -o hmmMiscFunctions.o
hmmMiscFunctions.c:236:49: warning: format specifies type 'int' but the argument has type 'double' [-Wformat]
Assertion about to fail! logPP= %d\n", logPP);
~~ ^~~~~
%f
hmmMiscFunctions.c:274:27: error: call to undeclared function 'Calloc'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
double *shape= (double*)Calloc(1, double);
^
hmmMiscFunctions.c:274:37: error: expected expression
double *shape= (double*)Calloc(1, double);
^
hmmMiscFunctions.c:275:37: error: expected expression
double *scale= (double*)Calloc(1, double);
^
hmmMiscFunctions.c:287:3: error: call to undeclared function 'Free'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
Free(shape);
^
hmmMiscFunctions.c:287:3: note: did you mean 'free'?
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/malloc/_malloc.h:42:7: note: 'free' declared here
void free(void *);
^
hmmMiscFunctions.c:384:10: warning: unused variable 'wi' [-Wunused-variable]
double wi, *newEx;
^
hmmMiscFunctions.c:417:10: warning: unused variable 'epsilon' [-Wunused-variable]
double epsilon=0.00001;
^
3 warnings and 4 errors generated.
make: *** [hmmMiscFunctions.o] Error 1
ERROR: compilation failed for package ‘groHMM’
* removing ‘/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpA2onxT/Rinst1216d61adc0b8/groHMM’
-----------------------------------
ERROR: package installation failed