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This page was generated on 2024-04-17 11:35:56 -0400 (Wed, 17 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4676
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4414
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4437
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 685/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
fabia 2.48.0  (landing page)
Andreas Mitterecker
Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024)
git_url: https://git.bioconductor.org/packages/fabia
git_branch: RELEASE_3_18
git_last_commit: 162c211
git_last_commit_date: 2023-10-24 09:44:16 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for fabia on nebbiolo2


To the developers/maintainers of the fabia package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/fabia.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.

raw results


Summary

Package: fabia
Version: 2.48.0
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:fabia.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings fabia_2.48.0.tar.gz
StartedAt: 2024-04-15 22:42:45 -0400 (Mon, 15 Apr 2024)
EndedAt: 2024-04-15 22:43:27 -0400 (Mon, 15 Apr 2024)
EllapsedTime: 41.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: fabia.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:fabia.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings fabia_2.48.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/fabia.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘fabia/DESCRIPTION’ ... OK
* this is package ‘fabia’ version ‘2.48.0’
* checking package namespace information ... OK
* checking package dependencies ... 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 ‘fabia’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* 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 ... 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 startup messages can be suppressed ... 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 ... NOTE
File ‘fabia/R/zzz.R’:
  .onLoad calls:
    packageStartupMessage("+----------------------------+                                          \n",     "|............................|                                          \n",     "|............................|                                          \n",     "|..............########......|  #######    #    ######    ###      #    \n",     "|..............########......|  #         # #   #     #    #      # #   \n",     "|.....####.....########......|  #        #   #  #     #    #     #   #  \n",     "|.....####.....########......|  #####   #     # ######     #    #     # \n",     "|.....####...................|  #       ####### #     #    #    ####### \n",     "|.....####...........###.....|  #       #     # #     #    #    #     # \n",     "|....................###.....|  #       #     # ######    ###   #     # \n",     "|....................###.....|                                          \n",     "|............................|                                          \n",     "+----------------------------+                                          \n")
    packageStartupMessage("Citation: S. Hochreiter et al.,", "\n",     "FABIA: Factor Analysis for Bicluster Acquisition,", "\n",     "Bioinformatics 26(12):1520-1527, 2010.", "\n", "BibTex: enter 'toBibtex(citation(\"fabia\"))'",     "\n\n", "Homepage: http://www.bioinf.jku.at/software/fabia/fabia.html",     "\n\n", "FABIA Package Version ", version, "\n")

See section ‘Good practice’ in '?.onAttach'.

plot,Factorization-missing: warning in symbols(ll[isel, 1], ll[isel,
  2], circle = sqs[isel], inches = FALSE, lwd = 3, add = TRUE, fg =
  colors[2]): partial argument match of 'circle' to 'circles'
plot,Factorization-missing: warning in symbols(zz[ii, 1], zz[ii, 2],
  square = sqs, inches = FALSE, lwd = 3, add = TRUE, fg = colors[2 +
  iGroup[i]]): partial argument match of 'square' to 'squares'
plot,Factorization-missing: no visible global function definition for
  ‘dev.new’
Undefined global functions or variables:
  dev.new
Consider adding
  importFrom("grDevices", "dev.new")
to your NAMESPACE file.
* checking Rd files ... WARNING
checkRd: (5) Factorization-class.Rd:346: \item in \arguments must have non-empty label
checkRd: (5) Factorization-class.Rd:398: \item in \arguments must have non-empty label
checkRd: (5) Factorization-class.Rd:401: \item in \arguments must have non-empty label
checkRd: (5) Factorization-class.Rd:402: \item in \arguments must have non-empty label
checkRd: (5) Factorization-class.Rd:408: \item in \arguments must have non-empty label
checkRd: (5) Factorization-class.Rd:409: \item in \arguments must have non-empty label
checkRd: (5) Factorization-class.Rd:410: \item in \arguments must have non-empty label
checkRd: (5) Factorization-class.Rd:416: \item in \value must have non-empty label
checkRd: (5) Factorization-class.Rd:417-418: \item in \value must have non-empty label
checkRd: (5) Factorization-class.Rd:419: \item in \value must have non-empty label
checkRd: (5) Factorization-class.Rd:424: \item in \value must have non-empty label
checkRd: (5) Factorization-class.Rd:425: \item in \value must have non-empty label
checkRd: (5) Factorization-class.Rd:426: \item in \value must have non-empty label
checkRd: (5) Factorization-class.Rd:427: \item in \value must have non-empty label
checkRd: (5) Factorization-class.Rd:428: \item in \value must have non-empty label
checkRd: (5) Factorization-class.Rd:429: \item in \value must have non-empty label
checkRd: (5) Factorization-class.Rd:167-177: \item in \describe must have non-empty label
checkRd: (5) Factorization-class.Rd:179-183: \item in \describe must have non-empty label
checkRd: (5) Factorization-class.Rd:185-189: \item in \describe must have non-empty label
checkRd: (5) Factorization-class.Rd:191-196: \item in \describe must have non-empty label
checkRd: (5) Factorization-class.Rd:198-203: \item in \describe must have non-empty label
checkRd: (5) Factorization-class.Rd:205-210: \item in \describe must have non-empty label
checkRd: (5) Factorization-class.Rd:212-217: \item in \describe must have non-empty label
checkRd: (5) Factorization-class.Rd:219-224: \item in \describe must have non-empty label
checkRd: (5) Factorization-class.Rd:226-231: \item in \describe must have non-empty label
checkRd: (5) Factorization-class.Rd:233-238: \item in \describe must have non-empty label
checkRd: (5) Factorization-class.Rd:240-245: \item in \describe must have non-empty label
checkRd: (5) Factorization-class.Rd:247-252: \item in \describe must have non-empty label
checkRd: (5) Factorization-class.Rd:254-259: \item in \describe must have non-empty label
checkRd: (5) Factorization-class.Rd:261-267: \item in \describe must have non-empty label
checkRd: (5) Factorization-class.Rd:269-275: \item in \describe must have non-empty label
checkRd: (5) Factorization-class.Rd:277-283: \item in \describe must have non-empty label
checkRd: (5) Factorization-class.Rd:285-290: \item in \describe must have non-empty label
checkRd: (5) Factorization-class.Rd:292-298: \item in \describe must have non-empty label
checkRd: (5) fabi.Rd:66-82: \item in \value must have non-empty label
checkRd: (5) fabia.Rd:75-91: \item in \value must have non-empty label
checkRd: (5) fabiap.Rd:88-104: \item in \value must have non-empty label
checkRd: (5) fabias.Rd:77-93: \item in \value must have non-empty label
checkRd: (5) fabiasp.Rd:65-81: \item in \value must have non-empty label
checkRd: (5) mfsc.Rd:75-83: \item in \value must have non-empty label
checkRd: (5) nmfdiv.Rd:49-55: \item in \value must have non-empty label
checkRd: (5) nmfeu.Rd:50-56: \item in \value must have non-empty label
checkRd: (5) nmfsc.Rd:76-82: \item in \value must have non-empty label
checkRd: (5) readSpfabiaResult.Rd:24-35: \item in \value must have non-empty label
checkRd: (5) samplesPerFeature.Rd:46-51: \item in \value must have non-empty label
checkRd: (5) spfabia.Rd:113-124: \item in \value must have non-empty label
* 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 line endings in shell scripts ... 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 include directives in Makefiles ... NOTE
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/Makefile.win
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.18-bioc/R/site-library/fabia/libs/fabia.so’:
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)

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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘fabia.Rnw’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/fabia.Rcheck/00check.log’
for details.



Installation output

fabia.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL fabia
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘fabia’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c fabiac.c -o fabiac.o
gcc -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o fabia.so fabiac.o -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.18-bioc/R/site-library/00LOCK-fabia/00new/fabia/libs
** R
** demo
** 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 (fabia)

Tests output


Example timings

fabia.Rcheck/fabia-Ex.timings

nameusersystemelapsed
Factorization-class0.5780.0290.606
estimateMode0.0020.0000.001
extractBic0.0410.0000.041
extractPlot0.1320.0030.135
fabi0.0870.0040.091
fabia0.0380.0070.046
fabiaDemo000
fabiaVersion0.0010.0000.000
fabiap0.0430.0000.043
fabias0.0430.0000.043
fabiasp0.1960.0120.208
makeFabiaData0.0330.0000.033
makeFabiaDataBlocks0.0350.0040.040
makeFabiaDataBlocksPos0.0340.0040.038
makeFabiaDataPos0.0390.0000.039
matrixImagePlot0.0390.0000.039
mfsc0.0580.0030.062
nmfdiv0.0380.0040.042
nmfeu0.0350.0080.043
nmfsc0.030.000.03
plotBicluster0.0720.0000.072
projFunc0.0010.0000.001
projFuncPos000
readSamplesSpfabia000
samplesPerFeature000
spfabia0.0380.0040.042