| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-26 06:18:06 -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 CNORode package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CNORode.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 375/2197 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CNORode 1.43.0 (landing page) Attila Gabor
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | |||||||||
| Package: CNORode |
| Version: 1.43.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:CNORode.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings CNORode_1.43.0.tar.gz |
| StartedAt: 2023-05-26 04:36:35 -0000 (Fri, 26 May 2023) |
| EndedAt: 2023-05-26 04:36:50 -0000 (Fri, 26 May 2023) |
| EllapsedTime: 15.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: CNORode.Rcheck |
| Warnings: NA |
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### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:CNORode.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings CNORode_1.43.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/CNORode.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 ‘CNORode/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CNORode’ version ‘1.43.0’
* 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
OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CNORode’ can be installed ... OK
* used C compiler: ‘gcc (GCC) 10.3.1’
* checking installed package size ... OK
* 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 ... 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 vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘CNORode-vignette.Rnw’ using ‘UTF-8’... failed to complete the test
ERROR
Errors in running code in vignettes:
when running code in ‘CNORode-vignette.Rnw’
...
> proc.time()
user system elapsed
0.190 0.011 0.196
... 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
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
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
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
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
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, 2 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/CNORode.Rcheck/00check.log’
for details.
CNORode.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL CNORode ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’ * installing *source* package ‘CNORode’ ... ** using staged installation ** libs using C compiler: ‘gcc (GCC) 10.3.1’ gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -g -O2 -c FG_transfer_function.c -o FG_transfer_function.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -g -O2 -c cvodea.c -o cvodea.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -g -O2 -c cvodea_io.c -o cvodea_io.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -g -O2 -c cvodes.c -o cvodes.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -g -O2 -c cvodes_band.c -o cvodes_band.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -g -O2 -c cvodes_bandpre.c -o cvodes_bandpre.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -g -O2 -c cvodes_bbdpre.c -o cvodes_bbdpre.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -g -O2 -c cvodes_dense.c -o cvodes_dense.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -g -O2 -c cvodes_diag.c -o cvodes_diag.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -g -O2 -c cvodes_direct.c -o cvodes_direct.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -g -O2 -c cvodes_io.c -o cvodes_io.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -g -O2 -c cvodes_spbcgs.c -o cvodes_spbcgs.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -g -O2 -c cvodes_spgmr.c -o cvodes_spgmr.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -g -O2 -c cvodes_spils.c -o cvodes_spils.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -g -O2 -c cvodes_sptfqmr.c -o cvodes_sptfqmr.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -g -O2 -c decimal2binary.c -o decimal2binary.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -g -O2 -c findStates.c -o findStates.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -g -O2 -c fnvector_serial.c -o fnvector_serial.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -g -O2 -c getAdjacencyMatrix.c -o getAdjacencyMatrix.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -g -O2 -c getNumBits.c -o getNumBits.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -g -O2 -c getNumInputs.c -o getNumInputs.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -g -O2 -c getStateIndex.c -o getStateIndex.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -g -O2 -c getTruthTables.c -o getTruthTables.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -g -O2 -c get_count_bits.c -o get_count_bits.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -g -O2 -c get_input_index.c -o get_input_index.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -g -O2 -c get_support_truth_tables.c -o get_support_truth_tables.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -g -O2 -c get_truth_tables_index.c -o get_truth_tables_index.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -g -O2 -c hill_function.c -o hill_function.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -g -O2 -c linear_transfer_function.c -o linear_transfer_function.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -g -O2 -c normHill.c -o normHill.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -g -O2 -c normHill_mod.c -o normHill_mod.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -g -O2 -c nvector_serial.c -o nvector_serial.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -g -O2 -c printAdjMat.c -o printAdjMat.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -g -O2 -c printInterMat.c -o printInterMat.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -g -O2 -c printNminiTerms.c -o printNminiTerms.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -g -O2 -c printTruthTables.c -o printTruthTables.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -g -O2 -c rhsODE.c -o rhsODE.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -g -O2 -c sim_logic_ode.c -o sim_logic_ode.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -g -O2 -c simulateODE.c -o simulateODE.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -g -O2 -c sundials_band.c -o sundials_band.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -g -O2 -c sundials_dense.c -o sundials_dense.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -g -O2 -c sundials_direct.c -o sundials_direct.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -g -O2 -c sundials_iterative.c -o sundials_iterative.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -g -O2 -c sundials_math.c -o sundials_math.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -g -O2 -c sundials_nvector.c -o sundials_nvector.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -g -O2 -c sundials_spbcgs.c -o sundials_spbcgs.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -g -O2 -c sundials_spgmr.c -o sundials_spgmr.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I./include -fPIC -g -O2 -c sundials_sptfqmr.c -o sundials_sptfqmr.o gcc -shared -L/home/biocbuild/R/R-4.3.0/lib -L/usr/local/lib -o CNORode.so FG_transfer_function.o cvodea.o cvodea_io.o cvodes.o cvodes_band.o cvodes_bandpre.o cvodes_bbdpre.o cvodes_dense.o cvodes_diag.o cvodes_direct.o cvodes_io.o cvodes_spbcgs.o cvodes_spgmr.o cvodes_spils.o cvodes_sptfqmr.o decimal2binary.o findStates.o fnvector_serial.o getAdjacencyMatrix.o getNumBits.o getNumInputs.o getStateIndex.o getTruthTables.o get_count_bits.o get_input_index.o get_support_truth_tables.o get_truth_tables_index.o hill_function.o linear_transfer_function.o normHill.o normHill_mod.o nvector_serial.o printAdjMat.o printInterMat.o printNminiTerms.o printTruthTables.o rhsODE.o sim_logic_ode.o simulateODE.o sundials_band.o sundials_dense.o sundials_direct.o sundials_iterative.o sundials_math.o sundials_nvector.o sundials_spbcgs.o sundials_spgmr.o sundials_sptfqmr.o -L/home/biocbuild/R/R-4.3.0/lib -lR installing to /home/biocbuild/R/R-4.3.0/site-library/00LOCK-CNORode/00new/CNORode/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 (CNORode)