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This page was generated on 2022-01-17 13:07:40 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
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

BUILD BIN results for gaga on machv2


To the developers/maintainers of the gaga package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gaga.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here 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 693/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gaga 2.40.0  (landing page)
David Rossell
Snapshot Date: 2022-01-16 01:55:05 -0500 (Sun, 16 Jan 2022)
git_url: https://git.bioconductor.org/packages/gaga
git_branch: RELEASE_3_14
git_last_commit: 8821347
git_last_commit_date: 2021-10-26 11:51:47 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  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: gaga
Version: 2.40.0
Command: rm -rf gaga.buildbin-libdir && mkdir gaga.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh gaga_2.40.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R gaga.buildbin-libdir
StartedAt: 2022-01-16 20:20:12 -0500 (Sun, 16 Jan 2022)
EndedAt: 2022-01-16 20:20:37 -0500 (Sun, 16 Jan 2022)
EllapsedTime: 25.0 seconds
RetCode: 0
Status:   OK  
PackageFile: gaga_2.40.0.tgz
PackageFileSize: 672.1 KiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf gaga.buildbin-libdir && mkdir gaga.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh gaga_2.40.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R gaga.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=gaga.buildbin-libdir gaga_2.40.0.tar.gz'
>>>>>>> 

* installing *source* package ‘gaga’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c cseqdesma.c -o cseqdesma.o
cseqdesma.c:4524:14: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
if ((*usesumx==0)) {                                               //if suff stat not pre-computed
     ~~~~~~~~^~~
cseqdesma.c:4524:14: note: remove extraneous parentheses around the comparison to silence this warning
if ((*usesumx==0)) {                                               //if suff stat not pre-computed
    ~        ^  ~
cseqdesma.c:4524:14: note: use '=' to turn this equality comparison into an assignment
if ((*usesumx==0)) {                                               //if suff stat not pre-computed
             ^~
             =
cseqdesma.c:5836:13: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
  if ((*usel==0)) {
       ~~~~~^~~
cseqdesma.c:5836:13: note: remove extraneous parentheses around the comparison to silence this warning
  if ((*usel==0)) {
      ~     ^  ~
cseqdesma.c:5836:13: note: use '=' to turn this equality comparison into an assignment
  if ((*usel==0)) {
            ^~
            =
cseqdesma.c:6070:13: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
  if ((*usel==0)) {
       ~~~~~^~~
cseqdesma.c:6070:13: note: remove extraneous parentheses around the comparison to silence this warning
  if ((*usel==0)) {
      ~     ^  ~
cseqdesma.c:6070:13: note: use '=' to turn this equality comparison into an assignment
  if ((*usel==0)) {
            ^~
            =
cseqdesma.c:6340:13: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
  if ((*usel==0)) {                                           //If l values have to be generated
       ~~~~~^~~
cseqdesma.c:6340:13: note: remove extraneous parentheses around the comparison to silence this warning
  if ((*usel==0)) {                                           //If l values have to be generated
      ~     ^  ~
cseqdesma.c:6340:13: note: use '=' to turn this equality comparison into an assignment
  if ((*usel==0)) {                                           //If l values have to be generated
            ^~
            =
4 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c cstat.c -o cstat.o
cstat.c:1838:6: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  if(abs(ndf - 2.0) < eps) {   /* df ~= 2 */
     ^
cstat.c:1838:6: note: use function 'fabs' instead
  if(abs(ndf - 2.0) < eps) {   /* df ~= 2 */
     ^~~
     fabs
cstat.c:18:19: warning: unused variable 'interface_c_sccs_id' [-Wunused-const-variable]
static const char interface_c_sccs_id[] = "%W%";
                  ^
cstat.c:19:19: warning: unused variable 'mess_c_sccs_id' [-Wunused-const-variable]
static const char mess_c_sccs_id[] = "%W%";
                  ^
cstat.c:20:19: warning: unused variable 'nrutil_c_sccs_id' [-Wunused-const-variable]
static const char nrutil_c_sccs_id[] = "%W%"; 
                  ^
cstat.c:21:19: warning: unused variable 'vector_c_sccs_id' [-Wunused-const-variable]
static const char vector_c_sccs_id[] = "%W%";
                  ^
cstat.c:22:19: warning: unused variable 'css_c_sccs_id' [-Wunused-const-variable]
static const char css_c_sccs_id[] = "@(#)$Workfile: rand.c$ $Revision: 5$";
                  ^
6 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 gaga.so cseqdesma.o cstat.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.14-bioc/meat/gaga.buildbin-libdir/00LOCK-gaga/00new/gaga/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 (gaga)


>>>>>>> 
>>>>>>> FIXING LINKS FOR gaga.buildbin-libdir/gaga/libs/gaga.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" "gaga.buildbin-libdir/gaga/libs/gaga.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libgfortran.5.dylib" "gaga.buildbin-libdir/gaga/libs/gaga.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libquadmath.0.dylib" "gaga.buildbin-libdir/gaga/libs/gaga.so"