Dario Strbenac
| Snapshot Date: 2025-04-24 15:01 -0400 (Thu, 24 Apr 2025) |
| git_url: https://git.bioconductor.org/packages/ClassifyR |
| git_branch: RELEASE_3_21 |
| git_last_commit: f3e8aad |
| git_last_commit_date: 2025-04-15 10:32:58 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-04-28 13:00 -0400 (Mon, 28 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4832 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" | 4574 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4558 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.0 RC (2025-04-04 r88129) -- "How About a Twenty-Six" | 4553 |
| 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 365/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ClassifyR 3.12.0 (landing page) Dario Strbenac
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | ERROR | |||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | ERROR | |||||||||
|
To the developers/maintainers of the ClassifyR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ClassifyR.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: ClassifyR |
| Version: 3.12.0 |
| Command: rm -rf ClassifyR.buildbin-libdir && mkdir ClassifyR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ClassifyR_3.12.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R ClassifyR.buildbin-libdir |
| StartedAt: 2025-04-25 12:59:41 -0400 (Fri, 25 Apr 2025) |
| EndedAt: 2025-04-25 13:01:04 -0400 (Fri, 25 Apr 2025) |
| EllapsedTime: 82.9 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf ClassifyR.buildbin-libdir && mkdir ClassifyR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ClassifyR_3.12.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R ClassifyR.buildbin-libdir
###
##############################################################################
##############################################################################
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=ClassifyR.buildbin-libdir ClassifyR_3.12.0.tar.gz'
>>>>>>>
* installing *source* package ‘ClassifyR’ ...
** this is package ‘ClassifyR’ version ‘3.12.0’
** 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/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c coxformatrices.cpp -o coxformatrices.o
coxformatrices.cpp:24:16: warning: unused variable 'sclback3' [-Wunused-variable]
double sclback3=*sctest3;
^
coxformatrices.cpp:23:16: warning: unused variable 'sclback2' [-Wunused-variable]
double sclback2=*sctest2;
^
coxformatrices.cpp:81:9: warning: suggest braces around initialization of subobject [-Wmissing-braces]
NULL
^~~~
{ }
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/stddef.h:84:18: note: expanded from macro 'NULL'
# define NULL __null
^~~~~~
coxformatrices.cpp:528:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register int i,j;
^~~~~~~~~
coxformatrices.cpp:528:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register int i,j;
^~~~~~~~~
coxformatrices.cpp:529:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register double temp;
^~~~~~~~~
coxformatrices.cpp:569:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register double temp;
^~~~~~~~~
coxformatrices.cpp:570:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register int i,j,k;
^~~~~~~~~
coxformatrices.cpp:570:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register int i,j,k;
^~~~~~~~~
coxformatrices.cpp:570:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register int i,j,k;
^~~~~~~~~
coxformatrices.cpp:656:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register int i;
^~~~~~~~~
coxformatrices.cpp:657:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
register double **pointer;
^~~~~~~~~
12 warnings generated.
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 ClassifyR.so coxformatrices.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Users/biocbuild/bbs-3.21-bioc/meat/ClassifyR.buildbin-libdir/00LOCK-ClassifyR/00new/ClassifyR/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for ‘ROCplot’ with signature ‘"ClassifyResult"’: no definition for class “ClassifyResult”
** help
*** installing help indices
*** copying figures
** 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 (ClassifyR)
>>>>>>>
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR ClassifyR.buildbin-libdir/ClassifyR/libs/ClassifyR.so
>>>>>>>
>>>>>>> Paths before fix:
ClassifyR.buildbin-libdir/ClassifyR/libs/ClassifyR.so:
ClassifyR.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0)
/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/4.5-x86_64/Resources/lib/libgcc_s.1.1.dylib" "ClassifyR.buildbin-libdir/ClassifyR/libs/ClassifyR.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libgfortran.5.dylib" "ClassifyR.buildbin-libdir/ClassifyR/libs/ClassifyR.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libquadmath.0.dylib" "ClassifyR.buildbin-libdir/ClassifyR/libs/ClassifyR.so"
>>>>>>> Paths after fix:
ClassifyR.buildbin-libdir/ClassifyR/libs/ClassifyR.so:
ClassifyR.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0)
/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)
chown: ClassifyR.buildbin-libdir/ClassifyR/CITATION: Operation not permitted
chown: ClassifyR.buildbin-libdir/ClassifyR/NEWS.Rd: Operation not permitted
chown: ClassifyR.buildbin-libdir/ClassifyR/R/ClassifyR: Operation not permitted
chown: ClassifyR.buildbin-libdir/ClassifyR/R/ClassifyR.rdx: Operation not permitted
chown: ClassifyR.buildbin-libdir/ClassifyR/R/ClassifyR.rdb: Operation not permitted
chown: ClassifyR.buildbin-libdir/ClassifyR/R: Operation not permitted
chown: ClassifyR.buildbin-libdir/ClassifyR/Meta/vignette.rds: Operation not permitted
chown: ClassifyR.buildbin-libdir/ClassifyR/Meta/data.rds: Operation not permitted
chown: ClassifyR.buildbin-libdir/ClassifyR/Meta/links.rds: Operation not permitted
chown: ClassifyR.buildbin-libdir/ClassifyR/Meta/features.rds: Operation not permitted
chown: ClassifyR.buildbin-libdir/ClassifyR/Meta/nsInfo.rds: Operation not permitted
chown: ClassifyR.buildbin-libdir/ClassifyR/Meta/package.rds: Operation not permitted
chown: ClassifyR.buildbin-libdir/ClassifyR/Meta/hsearch.rds: Operation not permitted
chown: ClassifyR.buildbin-libdir/ClassifyR/Meta/Rd.rds: Operation not permitted
chown: ClassifyR.buildbin-libdir/ClassifyR/Meta: Operation not permitted
chown: ClassifyR.buildbin-libdir/ClassifyR/NAMESPACE: Operation not permitted
chown: ClassifyR.buildbin-libdir/ClassifyR/html/R.css: Operation not permitted
chown: ClassifyR.buildbin-libdir/ClassifyR/html/00Index.html: Operation not permitted
chown: ClassifyR.buildbin-libdir/ClassifyR/html: Operation not permitted
chown: ClassifyR.buildbin-libdir/ClassifyR/libs/ClassifyR.so: Operation not permitted
chown: ClassifyR.buildbin-libdir/ClassifyR/libs: Operation not permitted
chown: ClassifyR.buildbin-libdir/ClassifyR/DESCRIPTION: Operation not permitted
chown: ClassifyR.buildbin-libdir/ClassifyR/INDEX: Operation not permitted
chown: ClassifyR.buildbin-libdir/ClassifyR/doc/index.html: Operation not permitted
chown: ClassifyR.buildbin-libdir/ClassifyR/doc/DevelopersGuide.html: Operation not permitted
chown: ClassifyR.buildbin-libdir/ClassifyR/doc/ClassifyR.html: Operation not permitted
chown: ClassifyR.buildbin-libdir/ClassifyR/doc/DevelopersGuide.R: Operation not permitted
chown: ClassifyR.buildbin-libdir/ClassifyR/doc/ClassifyR.R: Operation not permitted
chown: ClassifyR.buildbin-libdir/ClassifyR/doc/DevelopersGuide.Rmd: Operation not permitted
chown: ClassifyR.buildbin-libdir/ClassifyR/doc/ClassifyR.Rmd: Operation not permitted
chown: ClassifyR.buildbin-libdir/ClassifyR/doc: Operation not permitted
chown: ClassifyR.buildbin-libdir/ClassifyR/data/HuRI.RData: Operation not permitted
chown: ClassifyR.buildbin-libdir/ClassifyR/data/asthma.RData: Operation not permitted
chown: ClassifyR.buildbin-libdir/ClassifyR/data/METABRICclinical.RData: Operation not permitted
chown: ClassifyR.buildbin-libdir/ClassifyR/data: Operation not permitted
chown: ClassifyR.buildbin-libdir/ClassifyR/help/AnIndex: Operation not permitted
chown: ClassifyR.buildbin-libdir/ClassifyR/help/aliases.rds: Operation not permitted
chown: ClassifyR.buildbin-libdir/ClassifyR/help/paths.rds: Operation not permitted
chown: ClassifyR.buildbin-libdir/ClassifyR/help/figures/ClassifyRsticker.png: Operation not permitted
chown: ClassifyR.buildbin-libdir/ClassifyR/help/figures: Operation not permitted
chown: ClassifyR.buildbin-libdir/ClassifyR/help/ClassifyR.rdx: Operation not permitted
chown: ClassifyR.buildbin-libdir/ClassifyR/help/ClassifyR.rdb: Operation not permitted
chown: ClassifyR.buildbin-libdir/ClassifyR/help: Operation not permitted
chown: ClassifyR.buildbin-libdir/ClassifyR: Operation not permitted