| Back to Build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-05-26 06:18:05 -0000 (Fri, 26 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4254 |
| 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: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 314/2197 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ChemmineR 3.53.0 (landing page) Thomas Girke
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | |||||||||
| Package: ChemmineR |
| Version: 3.53.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:ChemmineR.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings ChemmineR_3.53.0.tar.gz |
| StartedAt: 2023-05-26 04:35:46 -0000 (Fri, 26 May 2023) |
| EndedAt: 2023-05-26 04:35:58 -0000 (Fri, 26 May 2023) |
| EllapsedTime: 12.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: ChemmineR.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:ChemmineR.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings ChemmineR_3.53.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/ChemmineR.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘ChemmineR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChemmineR’ version ‘3.53.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
download from 'https://CRAN.R-project.org/src/contrib/PACKAGES' failed
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/bioc/src/contrib:
download from 'https://bioconductor.org/packages/3.17/bioc/src/contrib/PACKAGES' failed
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/annotation/src/contrib:
download from 'https://bioconductor.org/packages/3.17/data/annotation/src/contrib/PACKAGES' failed
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/experiment/src/contrib:
download from 'https://bioconductor.org/packages/3.17/data/experiment/src/contrib/PACKAGES' failed
NOTE
Package which this enhances but not available for checking: ‘ChemmineOB’
* 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 ‘ChemmineR’ can be installed ... OK
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘png’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... NOTE
Problems with news in ‘inst/NEWS.Rd’:
NEWS.Rd: Sections \title, and \name must exist and be unique in Rd files
* checking R 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 loading without being on the library search path ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘ChemmineR.Rmd’ using ‘UTF-8’... failed to complete the test
ERROR
Errors in running code in vignettes:
when running code in ‘ChemmineR.Rmd’
...
> proc.time()
user system elapsed
0.167 0.031 0.192
... incomplete output. Crash?
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... ERROR
Rd conversion errors:
Converting parsed Rd's to LaTeX Warning in close.connection(con) :
Problem closing connection: No space left on device
Warning in close.connection(con) :
Problem closing connection: No space left on device
Warning in close.connection(con) :
Problem closing connection: No space left on device
Error in writeLines(x, con, useBytes = TRUE, ...) :
Error writing to connection: No space left on device
* DONE
Status: 2 ERRORs, 3 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/ChemmineR.Rcheck/00check.log’
for details.
ChemmineR.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL ChemmineR
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’
* installing *source* package ‘ChemmineR’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/BH/include' -I/usr/local/include -DNO_MAIN -DNO_DEBUG -fPIC -g -O2 -c DisjointSets.cpp -o DisjointSets.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/BH/include' -I/usr/local/include -DNO_MAIN -DNO_DEBUG -fPIC -g -O2 -c cluster.cc -o cluster.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/BH/include' -I/usr/local/include -DNO_MAIN -DNO_DEBUG -fPIC -g -O2 -c cstrsplit.cc -o cstrsplit.o
In file included from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/bind/mem_fn.hpp:25,
from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/mem_fn.hpp:22,
from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/function/detail/prologue.hpp:18,
from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/function.hpp:30,
from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/algorithm/string/split.hpp:16,
from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/algorithm/string.hpp:23,
from cstrsplit.cc:7:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/Rcpp.h:27,
from cstrsplit.cc:2:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/BH/include' -I/usr/local/include -DNO_MAIN -DNO_DEBUG -fPIC -g -O2 -c desc.cc -o desc.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/BH/include' -I/usr/local/include -DNO_MAIN -DNO_DEBUG -fPIC -g -O2 -c fingerprints.cc -o fingerprints.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/BH/include' -I/usr/local/include -DNO_MAIN -DNO_DEBUG -fPIC -g -O2 -c formats.cc -o formats.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/BH/include' -I/usr/local/include -DNO_MAIN -DNO_DEBUG -fPIC -g -O2 -c molecule.cc -o molecule.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/BH/include' -I/usr/local/include -DNO_MAIN -DNO_DEBUG -fPIC -g -O2 -c r_wrap.cc -o r_wrap.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/BH/include' -I/usr/local/include -DNO_MAIN -DNO_DEBUG -fPIC -g -O2 -c script.cc -o script.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/BH/include' -I/usr/local/include -DNO_MAIN -DNO_DEBUG -fPIC -g -O2 -c similarity.cc -o similarity.o
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.3.0/lib -L/usr/local/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 -L/home/biocbuild/R/R-4.3.0/lib -lR
installing to /home/biocbuild/R/R-4.3.0/site-library/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)