##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:SMAP.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings SMAP_1.66.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/SMAP.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 ‘SMAP/DESCRIPTION’ ... OK
* this is package ‘SMAP’ version ‘1.66.0’
* 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 ‘SMAP’ 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 ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
'library' or 'require' call to ‘methods’ which was already attached by Depends.
  Please remove these calls from your code.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘SMAP/R/AllClasses.R’:
  .onLoad calls:
    require("methods", quietly = TRUE)

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.

.draw.dist,gaussparam: no visible global function definition for
  ‘abline’
plot,SMAPObservations-missing: no visible global function definition
  for ‘par’
plot,SMAPObservations-missing: no visible global function definition
  for ‘points’
plot,SMAPObservations-missing: no visible global function definition
  for ‘abline’
plot,SMAPObservations-missing: no visible global function definition
  for ‘box’
plot,SMAPObservations-missing: no visible global function definition
  for ‘axis’
profilePlot,SMAPProfile: no visible global function definition for
  ‘par’
profilePlot,SMAPProfile: no visible global function definition for
  ‘points’
profilePlot,SMAPProfile: no visible global function definition for
  ‘abline’
profilePlot,SMAPProfile: no visible global function definition for
  ‘box’
profilePlot,SMAPProfile: no visible global function definition for
  ‘axis’
profilePlot,SMAPProfiles: no visible global function definition for
  ‘par’
profilePlot,SMAPProfiles: no visible global function definition for
  ‘abline’
profilePlot,SMAPProfiles: no visible global function definition for
  ‘box’
profilePlot,SMAPProfiles: no visible global function definition for
  ‘axis’
Undefined global functions or variables:
  abline axis box par points
Consider adding
  importFrom("graphics", "abline", "axis", "box", "par", "points")
to your NAMESPACE file.
* 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 compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
      user system elapsed
smap 5.973  0.049   6.021
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘SMAP.Rnw’... OK
 OK
* checking re-building of vignette outputs ... NOTE
Error(s) in re-building vignettes:
  ...
--- re-building ‘SMAP.Rnw’ using Sweave
Error: processing vignette 'SMAP.Rnw' failed with diagnostics:
cannot open file 'figs/fig-003.pdf'
--- failed re-building ‘SMAP.Rnw’

SUMMARY: processing the following file failed:
  ‘SMAP.Rnw’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/SMAP.Rcheck/00check.log’
for details.

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


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘SMAP’ ...
** 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 gradient.c -o gradient.o
gradient.c: In function ‘prior_gradient’:
gradient.c:142:21: warning: variable ‘lower’ set but not used [-Wunused-but-set-variable]
  142 |                 int lower;
      |                     ^~~~~
gradient.c: In function ‘hmm_update’:
gradient.c:247:24: warning: unused variable ‘tmp’ [-Wunused-variable]
  247 |                 double tmp;
      |                        ^~~
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c overlap.c -o overlap.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c prob.c -o prob.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c viterbi.c -o viterbi.o
gcc -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o SMAP.so gradient.o init.o overlap.o prob.o viterbi.o -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.18-bioc/R/site-library/00LOCK-SMAP/00new/SMAP/libs
** R
** data
** 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 (SMAP)