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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:PICS.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings PICS_2.51.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/PICS.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* 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 ‘PICS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PICS’ version ‘2.51.0’
* 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:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘PICS’ 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 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 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 compiled code ... NOTE
Note: information on .o files is not available
File ‘PICS/libs/PICS.so’:
  Found non-API call to R: ‘STRING_PTR’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/PICS.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL PICS
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘PICS’ ...
** using staged installation
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GSL... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c pics.c -o pics.o
pics.c: In function ‘ECM2’:
pics.c:1009:16: warning: variable ‘chiSum’ set but not used [-Wunused-but-set-variable]
 1009 |         double chiSum, etaF, etaR, dd, cc;
      |                ^~~~~~
pics.c: In function ‘getInfMat’:
pics.c:1633:83: warning: unused variable ‘PhiRw’ [-Wunused-variable]
 1633 |           double aNormF, aNormR, bNormF, bNormR, P0F=1, P0R=1, PhiF, PhiR, PhiFw, PhiRw, wPjF, wPjR;
      |                                                                                   ^~~~~
pics.c:1633:76: warning: unused variable ‘PhiFw’ [-Wunused-variable]
 1633 |           double aNormF, aNormR, bNormF, bNormR, P0F=1, P0R=1, PhiF, PhiR, PhiFw, PhiRw, wPjF, wPjR;
      |                                                                            ^~~~~
pics.c: In function ‘mergePeak’:
pics.c:1889:11: warning: unused variable ‘j’ [-Wunused-variable]
 1889 |   int i=0,j=0,k=0,l=0,kMerge=0,flag=0;
      |           ^
pics.c:1889:7: warning: unused variable ‘i’ [-Wunused-variable]
 1889 |   int i=0,j=0,k=0,l=0,kMerge=0,flag=0;
      |       ^
pics.c: In function ‘BIC’:
pics.c:1307:13: warning: ‘penalty’ may be used uninitialized [-Wmaybe-uninitialized]
 1307 |         bic = logDensityMix(yF, w, muF, sigmaSqF, K, NF) + logDensityMix(yR, w, muR, sigmaSqR, K,NR) - penalty;
      |         ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pics.c:1275:42: note: ‘penalty’ was declared here
 1275 |         double bic, tmp, muF[K], muR[K], penalty, distance;
      |                                          ^~~~~~~
pics.c: In function ‘fitModelK’:
pics.c:494:23: warning: ‘firstFit’ may be used uninitialized [-Wmaybe-uninitialized]
  494 |                 return(ans);
      |                       ^
pics.c:421:25: note: ‘firstFit’ was declared here
  421 |         SEXP ans, temp, firstFit;
      |                         ^~~~~~~~
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c segment.c -o segment.o
segment.c: In function ‘getDensity’:
segment.c:1494:19: warning: variable ‘chr’ set but not used [-Wunused-but-set-variable]
 1494 |   SEXP ans, x, y, chr, names;
      |                   ^~~
segment.c:1490:8: warning: unused variable ‘filter1’ [-Wunused-variable]
 1490 |   SEXP filter1;
      |        ^~~~~~~
segment.c:1489:11: warning: unused variable ‘muFilter’ [-Wunused-variable]
 1489 |   double *muFilter, *deltaFilter, *sFFilter, *sRFilter, *seFilter, *seFilterF, *seFilterR, *scoreFilter, *score;
      |           ^~~~~~~~
gcc -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o PICS.so pics.o segment.o -lgsl -lgslcblas -lm -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-PICS/00new/PICS/libs
** R
** 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 (PICS)