| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-26 06:18:15 -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 sangeranalyseR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/sangeranalyseR.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 1775/2197 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| sangeranalyseR 1.11.0 (landing page) Kuan-Hao Chao
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | |||||||||
| Package: sangeranalyseR |
| Version: 1.11.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:sangeranalyseR.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings sangeranalyseR_1.11.0.tar.gz |
| StartedAt: 2023-05-26 04:55:41 -0000 (Fri, 26 May 2023) |
| EndedAt: 2023-05-26 04:55:57 -0000 (Fri, 26 May 2023) |
| EllapsedTime: 16.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: sangeranalyseR.Rcheck |
| Warnings: NA |
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### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:sangeranalyseR.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings sangeranalyseR_1.11.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/sangeranalyseR.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 ‘sangeranalyseR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sangeranalyseR’ version ‘1.11.0’
* package encoding: UTF-8
* 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
Depends: includes the non-default packages:
'stringr', 'ape', 'Biostrings', 'DECIPHER', 'parallel', 'reshape2',
'phangorn', 'sangerseqR', 'gridExtra', 'shiny', 'shinydashboard',
'shinyjs', 'data.table', 'plotly', 'DT', 'zeallot', 'excelR',
'shinycssloaders', 'ggdendro', 'shinyWidgets', 'openxlsx', 'tools',
'rmarkdown', 'knitr', 'seqinr', 'BiocStyle', 'logger'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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
docs/build/html/.buildinfo
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... WARNING
Found the following file with a non-portable file name:
docs/wallpaperflare.com_wallpaper (1).jpg
These are not fully portable file names.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
Found the following non-portable file paths:
sangeranalyseR/docs/build/html/_downloads/081987116457968e1b81ae1616525c7d/Sanger_contigs_unalignment.fa
sangeranalyseR/docs/build/html/_downloads/13b875bc704f73b8bd67dc07d86fc474/Sanger_contigs_alignment.fa
sangeranalyseR/docs/build/html/_downloads/144d09562ae5b2c7dc079e4bc2b33fb7/Sanger_contigs_alignment.fa
sangeranalyseR/docs/build/html/_downloads/165af37e8893cfdfa4dba91c44cd791b/Sanger_contigs_unalignment.fa
sangeranalyseR/docs/build/html/_downloads/345ac400befc4f176c75732770ec3fcb/Achl_RBNII384-13_contig.fa
sangeranalyseR/docs/build/html/_downloads/438c8bd47d93d92c65b35b613ef14739/Sanger_all_trimmed_reads.fa
sangeranalyseR/docs/build/html/_downloads/6211ea1e7e3ccc1fcc9b74b78224eab6/Achl_ACHLO006-09_reads_unalignment.fa
sangeranalyseR/docs/build/html/_downloads/67bcad64cca804ec2e14cc42d016c08f/Achl_ACHLO006-09_reads_alignment.fa
sangeranalyseR/docs/build/html/_downloads/81a7338101f110748cb72056d9975225/Sanger_all_trimmed_reads.fa
sangeranalyseR/docs/build/html/_downloads/95ef9378c1407481d69c3bf882a580bb/Achl_RBNII384-13_reads_unalignment.fa
sangeranalyseR/docs/build/html/_downloads/a664bed9cc5d32924dc2ce60f8c60554/Sanger_all_trimmed_reads.fa
sangeranalyseR/docs/build/html/_downloads/b608796fffaaa7335a7341cffc9a9db7/Achl_ACHLO006-09_contig.fa
sangeranalyseR/docs/build/html/_downloads/b6b18aa3e34c6ae0be86c3940972dd38/Sanger_contigs_alignment.fa
sangeranalyseR/docs/build/html/_downloads/eeb554b575ee5b29ef733dafbf876c36/Achl_RBNII384-13_reads_alignment.fa
sangeranalyseR/docs/build/html/_downloads/fef71e7b2e1e49c01df301435e972047/Sanger_contigs_unalignment.fa
Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘sangeranalyseR’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 8.5Mb
sub-directories of 1Mb or more:
data 2.2Mb
extdata 5.5Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* 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 Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... 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 ...
‘sangeranalyseR.Rmd’ using ‘UTF-8’... failed to complete the test
ERROR
Errors in running code in vignettes:
when running code in ‘sangeranalyseR.Rmd’
...
> proc.time()
user system elapsed
0.177 0.019 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
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
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, 1 WARNING, 4 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/sangeranalyseR.Rcheck/00check.log’
for details.
sangeranalyseR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL sangeranalyseR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’ * installing *source* package ‘sangeranalyseR’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Note: wrong number of arguments to '==' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (sangeranalyseR)