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This page was generated on 2022-06-24 11:08:18 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4331
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4136
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4147
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

INSTALL results for oligo on lconway


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.

raw results

Package 1339/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
oligo 1.61.0  (landing page)
Benilton Carvalho
Snapshot Date: 2022-06-23 14:00:04 -0400 (Thu, 23 Jun 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)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: oligo
Version: 1.61.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL oligo
StartedAt: 2022-06-23 15:21:27 -0400 (Thu, 23 Jun 2022)
EndedAt: 2022-06-23 15:22:05 -0400 (Thu, 23 Jun 2022)
EllapsedTime: 38.4 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL oligo
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘oligo’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/preprocessCore/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c DABG.c -o DABG.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/preprocessCore/include' -I/usr/local/include   -fPIC  -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 -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/preprocessCore/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ParserXYS.c -o ParserXYS.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/preprocessCore/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c baseProfile.c -o baseProfile.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/preprocessCore/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c basecontent.c -o basecontent.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/preprocessCore/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c chipbackground.c -o chipbackground.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/preprocessCore/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c mas5calls.c -o mas5calls.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/preprocessCore/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c rma2.c -o rma2.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/preprocessCore/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c rma_common.c -o rma_common.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/preprocessCore/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c trimmed.c -o trimmed.o
clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/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/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -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
ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0'
ld: warning: dylib (/usr/local/gfortran/lib/libgfortran.dylib) was built for newer macOS version (12.0) than being linked (10.13)
ld: warning: dylib (/usr/local/gfortran/lib/libquadmath.dylib) was built for newer macOS version (12.0) than being linked (10.13)
installing to /Library/Frameworks/R.framework/Versions/4.2/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)