Philipp Angerer
| Snapshot Date: 2024-05-24 14:05:03 -0400 (Fri, 24 May 2024) |
| git_url: https://git.bioconductor.org/packages/destiny |
| git_branch: devel |
| git_last_commit: 3aca834 |
| git_last_commit_date: 2024-04-30 11:40:02 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-05-26 11:35:13 -0400 (Sun, 26 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4665 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4427 |
| 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 545/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| destiny 3.19.0 (landing page) Philipp Angerer
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the destiny package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/destiny.git to reflect on this report. See Troubleshooting Build Report for more information. - 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: destiny |
| Version: 3.19.0 |
| Command: rm -rf destiny.buildbin-libdir && mkdir destiny.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh destiny_3.19.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R destiny.buildbin-libdir |
| StartedAt: 2024-05-25 17:08:16 -0400 (Sat, 25 May 2024) |
| EndedAt: 2024-05-25 17:10:17 -0400 (Sat, 25 May 2024) |
| EllapsedTime: 120.9 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: destiny_3.19.0.tgz |
| PackageFileSize: 1.757 MiB |
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### Running command:
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### rm -rf destiny.buildbin-libdir && mkdir destiny.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh destiny_3.19.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R destiny.buildbin-libdir
###
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=destiny.buildbin-libdir destiny_3.19.0.tar.gz'
>>>>>>>
* installing *source* package ‘destiny’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/grDevices/include' -I/opt/R/x86_64/include -ggdb -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/grDevices/include' -I/opt/R/x86_64/include -ggdb -fPIC -falign-functions=64 -Wall -g -O2 -c censoring.cpp -o censoring.o
censoring.cpp:60:15: warning: variable 'm0' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
} else if (!one_uncertain && one_missing) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
censoring.cpp:71:20: note: uninitialized use occurs here
* ( std::erfc((m0-v) / sigma) - std::erfc((m1-v) / sigma) )
^~
censoring.cpp:60:11: note: remove the 'if' if its condition is always true
} else if (!one_uncertain && one_missing) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
censoring.cpp:60:15: warning: variable 'm0' is used uninitialized whenever '&&' condition is false [-Wsometimes-uninitialized]
} else if (!one_uncertain && one_missing) {
^~~~~~~~~~~~~~
censoring.cpp:71:20: note: uninitialized use occurs here
* ( std::erfc((m0-v) / sigma) - std::erfc((m1-v) / sigma) )
^~
censoring.cpp:60:15: note: remove the '&&' if its condition is always true
} else if (!one_uncertain && one_missing) {
^~~~~~~~~~~~~~~~~
censoring.cpp:55:13: note: initialize the variable 'm0' to silence this warning
double m0, m1;
^
= 0.0
censoring.cpp:60:15: warning: variable 'm1' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
} else if (!one_uncertain && one_missing) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
censoring.cpp:71:48: note: uninitialized use occurs here
* ( std::erfc((m0-v) / sigma) - std::erfc((m1-v) / sigma) )
^~
censoring.cpp:60:11: note: remove the 'if' if its condition is always true
} else if (!one_uncertain && one_missing) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
censoring.cpp:60:15: warning: variable 'm1' is used uninitialized whenever '&&' condition is false [-Wsometimes-uninitialized]
} else if (!one_uncertain && one_missing) {
^~~~~~~~~~~~~~
censoring.cpp:71:48: note: uninitialized use occurs here
* ( std::erfc((m0-v) / sigma) - std::erfc((m1-v) / sigma) )
^~
censoring.cpp:60:15: note: remove the '&&' if its condition is always true
} else if (!one_uncertain && one_missing) {
^~~~~~~~~~~~~~~~~
censoring.cpp:55:17: note: initialize the variable 'm1' to silence this warning
double m0, m1;
^
= 0.0
censoring.cpp:60:15: warning: variable 'use_d' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
} else if (!one_uncertain && one_missing) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
censoring.cpp:66:21: note: uninitialized use occurs here
const double v = use_d ? d : c;
^~~~~
censoring.cpp:60:11: note: remove the 'if' if its condition is always true
} else if (!one_uncertain && one_missing) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
censoring.cpp:60:15: warning: variable 'use_d' is used uninitialized whenever '&&' condition is false [-Wsometimes-uninitialized]
} else if (!one_uncertain && one_missing) {
^~~~~~~~~~~~~~
censoring.cpp:66:21: note: uninitialized use occurs here
const double v = use_d ? d : c;
^~~~~
censoring.cpp:60:15: note: remove the '&&' if its condition is always true
} else if (!one_uncertain && one_missing) {
^~~~~~~~~~~~~~~~~
censoring.cpp:18:12: note: initialize the variable 'use_d' to silence this warning
bool use_d;
^
= false
6 warnings generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/grDevices/include' -I/opt/R/x86_64/include -ggdb -fPIC -falign-functions=64 -Wall -g -O2 -c utils.cpp -o utils.o
clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o destiny.so RcppExports.o censoring.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.20-bioc/meat/destiny.buildbin-libdir/00LOCK-destiny/00new/destiny/libs
** R
** data
** demo
** 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 (destiny)
>>>>>>>
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR destiny.buildbin-libdir/destiny/libs/destiny.so
>>>>>>>
>>>>>>> Paths before fix:
destiny.buildbin-libdir/destiny/libs/destiny.so:
destiny.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
/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/4.4-x86_64/Resources/lib/libgcc_s.1.1.dylib" "destiny.buildbin-libdir/destiny/libs/destiny.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgfortran.5.dylib" "destiny.buildbin-libdir/destiny/libs/destiny.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libquadmath.0.dylib" "destiny.buildbin-libdir/destiny/libs/destiny.so"
>>>>>>> Paths after fix:
destiny.buildbin-libdir/destiny/libs/destiny.so:
destiny.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)