David Rossell
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/gaga |
| git_branch: RELEASE_3_17 |
| git_last_commit: 01ede91 |
| git_last_commit_date: 2023-04-25 09:46:13 -0400 (Tue, 25 Apr 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:02 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 | ||||
| Package 750/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| gaga 2.46.0 (landing page) David Rossell
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | WARNINGS | OK | | |||||||
|
To the developers/maintainers of the gaga package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: gaga |
| Version: 2.46.0 |
| Command: rm -rf gaga.buildbin-libdir && mkdir gaga.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh gaga_2.46.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R gaga.buildbin-libdir |
| StartedAt: 2023-10-19 13:29:14 -0400 (Thu, 19 Oct 2023) |
| EndedAt: 2023-10-19 13:29:48 -0400 (Thu, 19 Oct 2023) |
| EllapsedTime: 34.3 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: gaga_2.46.0.tgz |
| PackageFileSize: 765.2 KiB |
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### Running command:
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### rm -rf gaga.buildbin-libdir && mkdir gaga.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh gaga_2.46.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R gaga.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=gaga.buildbin-libdir gaga_2.46.0.tar.gz'
>>>>>>>
* installing *source* package ‘gaga’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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 -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -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 -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 gaga.so cseqdesma.o cstat.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.17-bioc-mac-arm64/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 PATHS TO DYNAMIC LIBRARIES FOR gaga.buildbin-libdir/gaga/libs/gaga.so
>>>>>>>
>>>>>>> Paths before fix:
gaga.buildbin-libdir/gaga/libs/gaga.so:
gaga.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgcc_s.1.1.dylib" "gaga.buildbin-libdir/gaga/libs/gaga.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/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/4.3-arm64/Resources/lib/libquadmath.0.dylib" "gaga.buildbin-libdir/gaga/libs/gaga.so"
>>>>>>> Paths after fix:
gaga.buildbin-libdir/gaga/libs/gaga.so:
gaga.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)