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This page was generated on 2021-10-15 15:06:48 -0400 (Fri, 15 Oct 2021).

BUILD BIN results for qrqc on machv2

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- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/qrqc.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
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raw results

Package 1475/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
qrqc 1.46.0  (landing page)
Vince Buffalo
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/qrqc
git_branch: RELEASE_3_13
git_last_commit: 891dd79
git_last_commit_date: 2021-05-19 11:48:11 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: qrqc
Version: 1.46.0
Command: rm -rf qrqc.buildbin-libdir && mkdir qrqc.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh qrqc_1.46.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R qrqc.buildbin-libdir
StartedAt: 2021-10-15 03:35:51 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 03:36:55 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 63.9 seconds
RetCode: 0
Status:   OK  
PackageFile: qrqc_1.46.0.tgz
PackageFileSize: 768.1 KiB

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf qrqc.buildbin-libdir && mkdir qrqc.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh qrqc_1.46.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R qrqc.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=qrqc.buildbin-libdir qrqc_1.46.0.tar.gz'
>>>>>>> 

* installing *source* package ‘qrqc’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_init_io.c -o R_init_io.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c io.c -o io.o
io.c:348:14: warning: incompatible pointer types initializing 'gzFile *' (aka 'struct gzFile_s **') with an expression of type 'gzFile' (aka 'struct gzFile_s *') [-Wincompatible-pointer-types]
  FILE_TYPE *fp = FILE_OPEN(CHAR(STRING_ELT(filename, 0)), "r");
             ^    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
io.c:351:21: warning: incompatible pointer types passing 'gzFile *' (aka 'struct gzFile_s **') to parameter of type 'gzFile' (aka 'struct gzFile_s *'); dereference with * [-Wincompatible-pointer-types]
  block = kseq_init(fp);
                    ^~
                    *
io.c:35:1: note: passing argument to parameter 'fd' here
KSEQ_INIT(gzFile, gzread)
^
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include/htslib/kseq.h:244:35: note: expanded from macro 'KSEQ_INIT'
#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
                                  ^
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include/htslib/kseq.h:241:2: note: expanded from macro 'KSEQ_INIT2'
        __KSEQ_BASIC(SCOPE, type_t)                                     \
        ^
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include/htslib/kseq.h:170:33: note: expanded from macro '__KSEQ_BASIC'
        SCOPE kseq_t *kseq_init(type_t fd)                                                                      \
                                       ^
io.c:453:21: warning: incompatible pointer types passing 'gzFile *' (aka 'struct gzFile_s **') to parameter of type 'gzFile' (aka 'struct gzFile_s *'); dereference with * [-Wincompatible-pointer-types]
  block = kseq_init(fp);
                    ^~
                    *
io.c:35:1: note: passing argument to parameter 'fd' here
KSEQ_INIT(gzFile, gzread)
^
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include/htslib/kseq.h:244:35: note: expanded from macro 'KSEQ_INIT'
#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
                                  ^
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include/htslib/kseq.h:241:2: note: expanded from macro 'KSEQ_INIT2'
        __KSEQ_BASIC(SCOPE, type_t)                                     \
        ^
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include/htslib/kseq.h:170:33: note: expanded from macro '__KSEQ_BASIC'
        SCOPE kseq_t *kseq_init(type_t fd)                                                                      \
                                       ^
io.c:454:14: warning: incompatible pointer types passing 'gzFile *' (aka 'struct gzFile_s **') to parameter of type 'gzFile' (aka 'struct gzFile_s *'); dereference with * [-Wincompatible-pointer-types]
  FILE_CLOSE(fp);
             ^~
             *
io.c:34:32: note: expanded from macro 'FILE_CLOSE'
#define FILE_CLOSE(x) (gzclose(x))
                               ^
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/zlib.h:1644:43: note: passing argument to parameter 'file' here
ZEXTERN int ZEXPORT    gzclose OF((gzFile file));
                                          ^
io.c:35:1: warning: unused function 'kseq_destroy' [-Wunused-function]
KSEQ_INIT(gzFile, gzread)
^
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include/htslib/kseq.h:244:35: note: expanded from macro 'KSEQ_INIT'
#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
                                  ^
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include/htslib/kseq.h:241:2: note: expanded from macro 'KSEQ_INIT2'
        __KSEQ_BASIC(SCOPE, type_t)                                     \
        ^
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include/htslib/kseq.h:176:13: note: expanded from macro '__KSEQ_BASIC'
        SCOPE void kseq_destroy(kseq_t *ks)                                                                     \
                   ^
5 warnings generated.
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 qrqc.so R_init_io.o io.o /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.13-bioc/meat/qrqc.buildbin-libdir/00LOCK-qrqc/00new/qrqc/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** 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 (qrqc)


>>>>>>> 
>>>>>>> FIXING LINKS FOR qrqc.buildbin-libdir/qrqc/libs/qrqc.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libgcc_s.1.dylib" "qrqc.buildbin-libdir/qrqc/libs/qrqc.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libgfortran.5.dylib" "qrqc.buildbin-libdir/qrqc/libs/qrqc.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libquadmath.0.dylib" "qrqc.buildbin-libdir/qrqc/libs/qrqc.so"