Thomas Girke
| Snapshot Date: 2022-07-06 14:00:06 -0400 (Wed, 06 Jul 2022) |
| git_url: https://git.bioconductor.org/packages/ChemmineR |
| git_branch: master |
| git_last_commit: 5214816 |
| git_last_commit_date: 2022-05-26 12:05:55 -0400 (Thu, 26 May 2022) |
| Back to Multiple platform build/check report for BioC 3.16 |
|
This page was generated on 2022-07-07 11:10:53 -0400 (Thu, 07 Jul 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" | 4343 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" | 4148 |
| lconway | macOS 12.2.1 Monterey | x86_64 | 4.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" | 4160 |
| kjohnson | macOS 12.4 Monterey | arm64 | 4.2.0 Patched (2022-06-09 r82473) -- "Vigorous Calisthenics" | 3115 |
| 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 | ||||
|
To the developers/maintainers of the ChemmineR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ChemmineR.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 298/2124 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ChemmineR 3.49.1 (landing page) Thomas Girke
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.2.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson | macOS 12.4 Monterey / arm64 | OK | OK | NA | ERROR | |||||||||
| Package: ChemmineR |
| Version: 3.49.1 |
| Command: rm -rf ChemmineR.buildbin-libdir && mkdir ChemmineR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ChemmineR_3.49.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R ChemmineR.buildbin-libdir |
| StartedAt: 2022-07-07 07:40:16 -0400 (Thu, 07 Jul 2022) |
| EndedAt: 2022-07-07 07:41:31 -0400 (Thu, 07 Jul 2022) |
| EllapsedTime: 74.7 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### rm -rf ChemmineR.buildbin-libdir && mkdir ChemmineR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ChemmineR_3.49.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R ChemmineR.buildbin-libdir
###
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=ChemmineR.buildbin-libdir ChemmineR_3.49.1.tar.gz'
>>>>>>>
* installing *source* package ‘ChemmineR’ ...
** using staged installation
** libs
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -DNO_MAIN -DNO_DEBUG -fPIC -falign-functions=64 -Wall -g -O2 -c DisjointSets.cpp -o DisjointSets.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -DNO_MAIN -DNO_DEBUG -fPIC -falign-functions=64 -Wall -g -O2 -c cluster.cc -o cluster.o
cluster.cc:49:13: warning: unused function 'prepare_neighbors' [-Wunused-function]
void static prepare_neighbors(const char* nbr_file, int skip, int p)
^
1 warning generated.
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -DNO_MAIN -DNO_DEBUG -fPIC -falign-functions=64 -Wall -g -O2 -c cstrsplit.cc -o cstrsplit.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -DNO_MAIN -DNO_DEBUG -fPIC -falign-functions=64 -Wall -g -O2 -c desc.cc -o desc.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -DNO_MAIN -DNO_DEBUG -fPIC -falign-functions=64 -Wall -g -O2 -c fingerprints.cc -o fingerprints.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -DNO_MAIN -DNO_DEBUG -fPIC -falign-functions=64 -Wall -g -O2 -c formats.cc -o formats.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -DNO_MAIN -DNO_DEBUG -fPIC -falign-functions=64 -Wall -g -O2 -c molecule.cc -o molecule.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -DNO_MAIN -DNO_DEBUG -fPIC -falign-functions=64 -Wall -g -O2 -c r_wrap.cc -o r_wrap.o
r_wrap.cc:563:7: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register size_t l = 0;
^~~~~~~~~
r_wrap.cc:564:7: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register size_t r = iter->size - 1;
^~~~~~~~~
r_wrap.cc:567:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register size_t i = (l + r) >> 1;
^~~~~~~~~
r_wrap.cc:570:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register int compare = strcmp(name, iname);
^~~~~~~~~
r_wrap.cc:614:7: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register size_t i = 0;
^~~~~~~~~
r_wrap.cc:633:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register const unsigned char *u = (unsigned char *) ptr;
^~~~~~~~~
r_wrap.cc:634:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register const unsigned char *eu = u + sz;
^~~~~~~~~
r_wrap.cc:636:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register unsigned char uu = *u;
^~~~~~~~~
r_wrap.cc:648:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register unsigned char *u = (unsigned char *) ptr;
^~~~~~~~~
r_wrap.cc:649:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register const unsigned char *eu = u + sz;
^~~~~~~~~
r_wrap.cc:651:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register char d = *(c++);
^~~~~~~~~
r_wrap.cc:652:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register unsigned char uu;
^~~~~~~~~
r_wrap.cc:949:15: warning: variable 'p' set but not used [-Wunused-but-set-variable]
const char *p = typeName;
^
r_wrap.cc:1689:14: warning: explicitly assigning value of variable of type 'void *' to itself [-Wself-assign]
clientdata = clientdata;
~~~~~~~~~~ ^ ~~~~~~~~~~
14 warnings generated.
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -DNO_MAIN -DNO_DEBUG -fPIC -falign-functions=64 -Wall -g -O2 -c script.cc -o script.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -DNO_MAIN -DNO_DEBUG -fPIC -falign-functions=64 -Wall -g -O2 -c similarity.cc -o similarity.o
clang++ -arch arm64 -std=gnu++14 -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 ChemmineR.so DisjointSets.o cluster.o cstrsplit.o desc.o fingerprints.o formats.o molecule.o r_wrap.o script.o similarity.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.16-bioc/meat/ChemmineR.buildbin-libdir/00LOCK-ChemmineR/00new/ChemmineR/libs
** R
** data
** 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 (ChemmineR)
>>>>>>>
>>>>>>> FIXING LINKS FOR ChemmineR.buildbin-libdir/ChemmineR/libs/ChemmineR.so
>>>>>>>
ERROR: R installation problem: File /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgcc_s.1.dylib not found!