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INSTALL report for qrqc on celaya2

This page was generated on 2019-10-16 12:48:51 -0400 (Wed, 16 Oct 2019).

Package 1288/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
qrqc 1.38.0
Vince Buffalo
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/qrqc
Branch: RELEASE_3_9
Last Commit: d6aef92
Last Changed Date: 2019-05-02 11:53:24 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64 [ OK ] OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: qrqc
Version: 1.38.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL qrqc
StartedAt: 2019-10-15 19:34:54 -0400 (Tue, 15 Oct 2019)
EndedAt: 2019-10-15 19:35:47 -0400 (Tue, 15 Oct 2019)
EllapsedTime: 53.3 seconds
RetCode: 0
Status:  OK 

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL qrqc
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘qrqc’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/Library/Frameworks/R.framework/Resources/bin/R" --vanilla --slave` -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c R_init_io.c -o R_init_io.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/Library/Frameworks/R.framework/Resources/bin/R" --vanilla --slave` -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/3.6/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/3.6/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/3.6/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/3.6/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/3.6/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/3.6/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/MacOSX.sdk/usr/include/zlib.h:1521:43: 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/3.6/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/3.6/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/3.6/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 -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/3.6/Resources/library/Rhtslib/usrlib/libhts.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/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)