Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-16 11:43 -0400 (Fri, 16 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4420 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4413 |
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 1417/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
NuPoP 2.13.0 (landing page) Ji-Ping Wang
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the NuPoP package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/NuPoP.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: NuPoP |
Version: 2.13.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:NuPoP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings NuPoP_2.13.0.tar.gz |
StartedAt: 2024-08-16 00:37:52 -0400 (Fri, 16 Aug 2024) |
EndedAt: 2024-08-16 00:44:15 -0400 (Fri, 16 Aug 2024) |
EllapsedTime: 383.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: NuPoP.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:NuPoP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings NuPoP_2.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/NuPoP.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘NuPoP/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘NuPoP’ version ‘2.13.0’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.19/bioc/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.19/data/annotation/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.19/data/annotation/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.19/data/experiment/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.19/data/experiment/src/contrib/PACKAGES' OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘NuPoP’ can be installed ... OK * used Fortran compiler: ‘GNU Fortran (GCC) 12.2.0’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... NOTE installed size is 5.7Mb sub-directories of 1Mb or more: R 3.3Mb extdata 2.2Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking R/sysdata.rda ... NOTE Note: significantly better compression could be obtained by using R CMD build --resave-data old_size new_size compress sysdata.rda 4.6Mb 2.9Mb xz * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available File ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/NuPoP/libs/NuPoP.so’: Found ‘__gfortran_st_close’, possibly from ‘close’ (Fortran) Found ‘__gfortran_st_open’, possibly from ‘open’ (Fortran) Found ‘__gfortran_st_read’, possibly from ‘read’ (Fortran) Found ‘__gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’ (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * checking usage of KIND in Fortran files ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/NuPoP.Rcheck/00check.log’ for details.
NuPoP.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL NuPoP ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘NuPoP’ ... ** using staged installation ** libs using Fortran compiler: ‘GNU Fortran (GCC) 12.2.0’ using SDK: ‘MacOSX11.3.sdk’ /opt/gfortran/bin/gfortran -arch x86_64 -fPIC -Wall -g -O2 -c cvtbfb.f90 -o cvtbfb.o /opt/gfortran/bin/gfortran -arch x86_64 -fPIC -Wall -g -O2 -c cvtbfbNL4.f90 -o cvtbfbNL4.o cvtbfbNL4.f90:13:51: 13 | real*8 freqN4(4,4,4,4),tranN4(5:147,4,4,4,4,4),freqL4(4,4,4,4) | 1 Warning: Array ‘trann4’ at (1) is larger than limit set by ‘-fmax-stack-var-size=’, moved from stack to static storage. This makes the procedure unsafe when called recursively, or concurrently from multiple threads. Consider increasing the ‘-fmax-stack-var-size=’ limit (or use ‘-frecursive’, which implies unlimited ‘-fmax-stack-var-size’) - or change the code to use an ALLOCATABLE array. If the variable is never accessed concurrently, this warning can be ignored, and the variable could also be declared with the SAVE attribute. [-Wsurprising] /opt/gfortran/bin/gfortran -arch x86_64 -fPIC -Wall -g -O2 -c vtbfb.f90 -o vtbfb.o /opt/gfortran/bin/gfortran -arch x86_64 -fPIC -Wall -g -O2 -c vtbfbNL4.f90 -o vtbfbNL4.o vtbfbNL4.f90:13:51: 13 | real*8 freqN4(4,4,4,4),tranN4(5:147,4,4,4,4,4),freqL4(4,4,4,4) | 1 Warning: Array ‘trann4’ at (1) is larger than limit set by ‘-fmax-stack-var-size=’, moved from stack to static storage. This makes the procedure unsafe when called recursively, or concurrently from multiple threads. Consider increasing the ‘-fmax-stack-var-size=’ limit (or use ‘-frecursive’, which implies unlimited ‘-fmax-stack-var-size’) - or change the code to use an ALLOCATABLE array. If the variable is never accessed concurrently, this warning can be ignored, and the variable could also be declared with the SAVE attribute. [-Wsurprising] clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o NuPoP.so cvtbfb.o cvtbfbNL4.o vtbfb.o vtbfbNL4.o -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-NuPoP/00new/NuPoP/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 (NuPoP)
NuPoP.Rcheck/NuPoP-Ex.timings
name | user | system | elapsed | |
NuPoP-package | 0 | 0 | 0 | |
plotNuPoP | 0.028 | 0.003 | 0.031 | |
predNuPoP | 1.159 | 0.013 | 1.173 | |
predNuPoP_chem | 1.182 | 0.009 | 1.192 | |
readNuPoP | 1.170 | 0.007 | 1.178 | |