##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:tweeDEseq.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings tweeDEseq_1.53.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/tweeDEseq.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'tweeDEseq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'tweeDEseq' version '1.53.0'
* package encoding: UTF-8
* 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 whether package 'tweeDEseq' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 13.3.0'
* 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 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  qqchisq.Rd: zscoreGamma
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'AIC.glmPT' 'L' 'anova.glmPT' 'format.perc' 'gammratio' 'getZhuParam'
  'hou2puig' 'k' 'k3' 'kappa3' 'kvector' 'logLik.glmPT' 'loglikGlm'
  'loglikPoissonTweedie3' 'logprobs' 'momentEstimates_wt_C' 'nprobs'
  'permtest' 'print.glmPT' 'puig2hou' 'summary.glmPT' 'zhu2hou'
  'zhuprobs'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 for x64 is not available
File 'E:/biocbuild/bbs-3.21-bioc/R/library/tweeDEseq/libs/x64/tweeDEseq.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  'E:/biocbuild/bbs-3.21-bioc/meat/tweeDEseq.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL tweeDEseq
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'tweeDEseq' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.3.0'
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cov_wt_C.c -o cov_wt_C.o
cov_wt_C.c: In function 'cov_wt_C':
cov_wt_C.c:79:14: warning: 'wvar' may be used uninitialized [-Wmaybe-uninitialized]
   79 |   free(aux), free(wvar), free(y);
      |              ^~~~~~~~~~
cov_wt_C.c:49:41: note: 'wvar' was declared here
   49 |   double *x, *z = REAL(Y), *res, *aux, *wvar, *y, sumY, h1;
      |                                         ^~~~
cov_wt_C.c: In function 'momentEstimates_wt_C':
cov_wt_C.c:154:12: warning: 'moments' may be used uninitialized [-Wmaybe-uninitialized]
  154 |   free(y), free(moments), free(aux);
      |            ^~~~~~~~~~~~~
cov_wt_C.c:116:21: note: 'moments' was declared here
  116 |   double *res, *x, *moments, d, kappa, resk, a, *z = REAL(Y), *y, sumY, *aux, h1;
      |                     ^~~~~~~
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c init_tweeDEseq.c -o init_tweeDEseq.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c loglikGlm.c -o loglikGlm.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c logprobs.c -o logprobs.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c permtest.c -o permtest.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c probs.c -o probs.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c zhu2.c -o zhu2.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c zhu3.c -o zhu3.o
gcc -shared -s -static-libgcc -o tweeDEseq.dll tmp.def cov_wt_C.o init_tweeDEseq.o loglikGlm.o logprobs.o permtest.o probs.o zhu2.o zhu3.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
installing to E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-tweeDEseq/00new/tweeDEseq/libs/x64
** R
** data
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (tweeDEseq)