Benilton Carvalho
| Snapshot Date: 2022-07-10 14:00:02 -0400 (Sun, 10 Jul 2022) |
| git_url: https://git.bioconductor.org/packages/oligo |
| git_branch: master |
| git_last_commit: d4b4e9e |
| git_last_commit_date: 2022-04-26 10:57:15 -0400 (Tue, 26 Apr 2022) |
| Back to Multiple platform build/check report for BioC 3.16 |
|
This page was generated on 2022-07-11 11:06:52 -0400 (Mon, 11 Jul 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4148 |
| lconway | macOS 12.2.1 Monterey | x86_64 | 4.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" | 4168 |
| kjohnson | macOS 12.4 Monterey | arm64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 3545 |
| 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 | ||||
|
To the developers/maintainers of the oligo package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/oligo.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1347/2130 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| oligo 1.61.0 (landing page) Benilton Carvalho
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| lconway | macOS 12.2.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson | macOS 12.4 Monterey / arm64 | OK | NA | NA | NA | |||||||||
| Package: oligo |
| Version: 1.61.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL oligo |
| StartedAt: 2022-07-10 16:14:53 -0400 (Sun, 10 Jul 2022) |
| EndedAt: 2022-07-10 16:16:21 -0400 (Sun, 10 Jul 2022) |
| EllapsedTime: 87.6 seconds |
| RetCode: 0 |
| Status: OK |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL oligo
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library’
* installing *source* package ‘oligo’ ...
** using staged installation
** libs
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c DABG.c -o DABG.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ParserGzXYS.c -o ParserGzXYS.o
ParserGzXYS.c:18:17: warning: incompatible pointer types passing 'gzFile *' (aka 'struct gzFile_s **') to parameter of type 'gzFile' (aka 'struct gzFile_s *'); dereference with * [-Wincompatible-pointer-types]
while (!gzeof(file)){
^~~~
*
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/zlib.h:1608:38: note: passing argument to parameter 'file' here
ZEXTERN int ZEXPORT gzeof OF((gzFile file));
^
ParserGzXYS.c:19:12: warning: incompatible pointer types passing 'gzFile *' (aka 'struct gzFile_s **') to parameter of type 'gzFile' (aka 'struct gzFile_s *'); dereference with * [-Wincompatible-pointer-types]
gzgets(file, buffer, 1000);
^~~~
*
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/zlib.h:1505:42: note: passing argument to parameter 'file' here
ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len));
^
ParserGzXYS.c:46:6: warning: incompatible pointer types assigning to 'gzFile *' (aka 'struct gzFile_s **') from 'gzFile' (aka 'struct gzFile_s *') [-Wincompatible-pointer-types]
fp = gzopen(currentFile, "rb");
^ ~~~~~~~~~~~~~~~~~~~~~~~~~
ParserGzXYS.c:50:10: warning: incompatible pointer types passing 'gzFile *' (aka 'struct gzFile_s **') to parameter of type 'gzFile' (aka 'struct gzFile_s *'); dereference with * [-Wincompatible-pointer-types]
gzgets(fp, buffer, LINEMAX);
^~
*
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/zlib.h:1505:42: note: passing argument to parameter 'file' here
ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len));
^
ParserGzXYS.c:51:11: warning: incompatible pointer types passing 'gzFile *' (aka 'struct gzFile_s **') to parameter of type 'gzFile' (aka 'struct gzFile_s *'); dereference with * [-Wincompatible-pointer-types]
gzclose(fp);
^~
*
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/zlib.h:1644:43: note: passing argument to parameter 'file' here
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
ParserGzXYS.c:134:6: warning: incompatible pointer types assigning to 'gzFile *' (aka 'struct gzFile_s **') from 'gzFile' (aka 'struct gzFile_s *') [-Wincompatible-pointer-types]
fp = gzopen(CHAR(STRING_ELT(filenames, 0)), "rb");
^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ParserGzXYS.c:138:11: warning: incompatible pointer types passing 'gzFile *' (aka 'struct gzFile_s **') to parameter of type 'gzFile' (aka 'struct gzFile_s *'); dereference with * [-Wincompatible-pointer-types]
gzclose(fp);
^~
*
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/zlib.h:1644:43: note: passing argument to parameter 'file' here
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
7 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ParserXYS.c -o ParserXYS.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c baseProfile.c -o baseProfile.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c basecontent.c -o basecontent.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c chipbackground.c -o chipbackground.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c mas5calls.c -o mas5calls.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rma2.c -o rma2.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rma_common.c -o rma_common.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c trimmed.c -o trimmed.o
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o oligo.so DABG.o ParserGzXYS.o ParserXYS.o baseProfile.o basecontent.o chipbackground.o mas5calls.o rma2.o rma_common.o trimmed.o -lz -L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1 -L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lquadmath -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/00LOCK-oligo/00new/oligo/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Note: in method for ‘pm<-’ with signature
‘object="TilingFeatureSet",subset="ANY",target="ANY",value="array"’:
expanding the signature to include omitted arguments in definition:
subset = "missing", target = "missing"
Note: in method for ‘mm<-’ with signature
‘object="TilingFeatureSet",subset="ANY",target="ANY",value="array"’:
expanding the signature to include omitted arguments in definition:
subset = "missing", target = "missing"
** 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 (oligo)