##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:fabia.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings fabia_2.52.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/fabia.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘fabia/DESCRIPTION’ ... OK
* this is package ‘fabia’ version ‘2.52.0’
* 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 13.2.0-23ubuntu4) 13.2.0’
* 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 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 loading without being on the library search path ... OK
* checking whether 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: (-1) Factorization-class.Rd:511: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) Factorization-class.Rd:512: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) Factorization-class.Rd:513: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) Factorization-class.Rd:514: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) Factorization-class.Rd:529: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) Factorization-class.Rd:530: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) Factorization-class.Rd:531: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) Factorization-class.Rd:532: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) Factorization-class.Rd:548: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) Factorization-class.Rd:550: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) Factorization-class.Rd:552: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) Factorization-class.Rd:554: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) Factorization-class.Rd:556: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) Factorization-class.Rd:558: Lost braces in \enumerate; meant \describe ?
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: (-1) Factorization-class.Rd:331: Lost braces
   331 | \item{plot}{\code{signature(x = "Factorization", y = "missing")}}{ Plot of a matrix factorization result}
       |                                                                  ^
checkRd: (-1) Factorization-class.Rd:333: Lost braces
   333 | \item{show}{\code{signature(object = "Factorization")}}{ Display statistics of a matrix factorization result}
       |                                                        ^
checkRd: (-1) Factorization-class.Rd:336-337: Lost braces
   336 |   "numeric")}}{ Display
       |               ^
checkRd: (-1) Factorization-class.Rd:339: Lost braces
   339 | \item{summary}{\code{signature(object = "Factorization")}}{ Summary of matrix factorization result}
       |                                                           ^
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: (-1) samplesPerFeature.Rd:49-50: Lost braces
    49 |   \code{nsL} {Vector of feature length containing number of samples
       |              ^
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 ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-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 ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 2 NOTEs
See
  ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/fabia.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL fabia
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘fabia’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c fabiac.c -o fabiac.o
fabiac.c: In function ‘readSpfabicResult’:
fabiac.c:3588:17: warning: argument 1 null where non-null expected [-Wnonnull]
 3588 |                 fclose (pFile);
      |                 ^~~~~~~~~~~~~~
In file included from fabiac.c:2:
/usr/include/stdio.h:184:12: note: in a call to function ‘fclose’ declared ‘nonnull’
  184 | extern int fclose (FILE *__stream) __nonnull ((1));
      |            ^~~~~~
gcc -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o fabia.so fabiac.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /media/volume/teran2_disk/biocbuild/bbs-3.20-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)