Renan Sauteraud
| Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/PICS |
| git_branch: devel |
| git_last_commit: 59be92f |
| git_last_commit_date: 2024-10-29 09:33:53 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-24 11:47 -0500 (Tue, 24 Dec 2024).
| 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" | 4754 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
| 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 1543/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| PICS 2.51.0 (landing page) Renan Sauteraud
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | ERROR | ERROR | skipped | |||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | 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 PICS package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PICS.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: PICS |
| Version: 2.51.0 |
| Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data PICS |
| StartedAt: 2024-12-24 01:23:19 -0000 (Tue, 24 Dec 2024) |
| EndedAt: 2024-12-24 01:23:24 -0000 (Tue, 24 Dec 2024) |
| EllapsedTime: 5.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data PICS
###
##############################################################################
##############################################################################
* checking for file ‘PICS/DESCRIPTION’ ... OK
* preparing ‘PICS’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* running ‘cleanup’
* installing the package to build vignettes
-----------------------------------
* installing *source* package ‘PICS’ ...
** using staged installation
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GSL... yes
configure: creating ./config.status
config.status: creating src/Makevars
** 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 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c pics.c -o pics.o
pics.c: In function ‘ECM2’:
pics.c:1009:16: warning: variable ‘chiSum’ set but not used [-Wunused-but-set-variable]
1009 | double chiSum, etaF, etaR, dd, cc;
| ^~~~~~
pics.c: In function ‘getInfMat’:
pics.c:1633:83: warning: unused variable ‘PhiRw’ [-Wunused-variable]
1633 | double aNormF, aNormR, bNormF, bNormR, P0F=1, P0R=1, PhiF, PhiR, PhiFw, PhiRw, wPjF, wPjR;
| ^~~~~
pics.c:1633:76: warning: unused variable ‘PhiFw’ [-Wunused-variable]
1633 | double aNormF, aNormR, bNormF, bNormR, P0F=1, P0R=1, PhiF, PhiR, PhiFw, PhiRw, wPjF, wPjR;
| ^~~~~
pics.c: In function ‘mergePeak’:
pics.c:1889:11: warning: unused variable ‘j’ [-Wunused-variable]
1889 | int i=0,j=0,k=0,l=0,kMerge=0,flag=0;
| ^
pics.c:1889:7: warning: unused variable ‘i’ [-Wunused-variable]
1889 | int i=0,j=0,k=0,l=0,kMerge=0,flag=0;
| ^
pics.c: In function ‘BIC’:
pics.c:1307:13: warning: ‘penalty’ may be used uninitialized [-Wmaybe-uninitialized]
1307 | bic = logDensityMix(yF, w, muF, sigmaSqF, K, NF) + logDensityMix(yR, w, muR, sigmaSqR, K,NR) - penalty;
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pics.c:1275:42: note: ‘penalty’ was declared here
1275 | double bic, tmp, muF[K], muR[K], penalty, distance;
| ^~~~~~~
pics.c: In function ‘fitModelK’:
pics.c:494:23: warning: ‘firstFit’ may be used uninitialized [-Wmaybe-uninitialized]
494 | return(ans);
| ^
pics.c:421:25: note: ‘firstFit’ was declared here
421 | SEXP ans, temp, firstFit;
| ^~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c segment.c -o segment.o
segment.c: In function ‘segReads’:
segment.c:147:22: error: implicit declaration of function ‘Calloc’; did you mean ‘calloc’? [-Wimplicit-function-declaration]
147 | scoreRegionF=(int*)Calloc((M-m)/(2*INTEGER_VALUE(width)), int);
| ^~~~~~
| calloc
segment.c:147:61: error: expected expression before ‘int’
147 | scoreRegionF=(int*)Calloc((M-m)/(2*INTEGER_VALUE(width)), int);
| ^~~
segment.c:148:61: error: expected expression before ‘int’
148 | scoreRegionR=(int*)Calloc((M-m)/(2*INTEGER_VALUE(width)), int);
| ^~~
segment.c: In function ‘getDensity’:
segment.c:1494:19: warning: variable ‘chr’ set but not used [-Wunused-but-set-variable]
1494 | SEXP ans, x, y, chr, names;
| ^~~
segment.c:1490:8: warning: unused variable ‘filter1’ [-Wunused-variable]
1490 | SEXP filter1;
| ^~~~~~~
segment.c:1489:11: warning: unused variable ‘muFilter’ [-Wunused-variable]
1489 | double *muFilter, *deltaFilter, *sFFilter, *sRFilter, *seFilter, *seFilterF, *seFilterR, *scoreFilter, *score;
| ^~~~~~~~
make: *** [/home/biocbuild/R/R/etc/Makeconf:195: segment.o] Error 1
ERROR: compilation failed for package ‘PICS’
* removing ‘/home/biocbuild/tmp/Rtmpkyj3Cp/Rinst373c035eb6af96/PICS’
-----------------------------------
ERROR: package installation failed