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This page was generated on 2024-06-11 14:40 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4522
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4468
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 773/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gaga 2.50.0  (landing page)
David Rossell
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/gaga
git_branch: RELEASE_3_19
git_last_commit: 7556a12
git_last_commit_date: 2024-04-30 10:17:33 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for gaga on palomino3

To the developers/maintainers of the gaga package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gaga.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: gaga
Version: 2.50.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:gaga.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings gaga_2.50.0.tar.gz
StartedAt: 2024-06-10 03:57:27 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 03:59:43 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 136.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: gaga.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:gaga.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings gaga_2.50.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/gaga.Rcheck'
* using R version 4.4.0 (2024-04-24 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 'gaga/DESCRIPTION' ... OK
* this is package 'gaga' version '2.50.0'
* 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 whether package 'gaga' can be installed ... WARNING
Found the following significant warnings:
  cstat.c:667:20: warning: the comparison will always evaluate as 'true' for the pointer operand in 'v + (sizetype)((long long unsigned int)nl * 4)' must not be NULL [-Waddress]
  cstat.c:673:20: warning: the comparison will always evaluate as 'true' for the pointer operand in 'v + (sizetype)((long long unsigned int)nl * 8)' must not be NULL [-Waddress]
  cstat.c:679:20: warning: the comparison will always evaluate as 'true' for the pointer operand in 'v + (sizetype)((long long unsigned int)nl * 4)' must not be NULL [-Waddress]
  cstat.c:687:47: warning: the comparison will always evaluate as 'true' for the pointer operand in '*(m + (sizetype)((long long unsigned int)i * 8)) + (sizetype)((long long unsigned int)ncl * 8)' must not be NULL [-Waddress]
  cstat.c:689:21: warning: the comparison will always evaluate as 'true' for the pointer operand in 'm + (sizetype)((long long unsigned int)nrl * 8)' must not be NULL [-Waddress]
  cstat.c:697:47: warning: the comparison will always evaluate as 'true' for the pointer operand in '*(m + (sizetype)((long long unsigned int)i * 8)) + (sizetype)((long long unsigned int)ncl * 4)' must not be NULL [-Waddress]
  cstat.c:699:21: warning: the comparison will always evaluate as 'true' for the pointer operand in 'm + (sizetype)((long long unsigned int)nrl * 8)' must not be NULL [-Waddress]
  cstat.c:1282:4: warning: 'lu_solve' accessing 8 bytes in a region of size 0 [-Wstringop-overflow=]
  cstat.c:4490:7: warning: 'dirmin' accessing 8 bytes in a region of size 0 [-Wstringop-overflow=]
  cstat.c:4505:9: warning: 'dirmin' accessing 8 bytes in a region of size 0 [-Wstringop-overflow=]
See 'F:/biocbuild/bbs-3.19-bioc/meat/gaga.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 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 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
adjustfitNN: no visible global function definition for 'predict'
checkfit.gagafit: no visible global function definition for 'is'
checkfit.gagafit: no visible global function definition for 'density'
checkfit.gagafit: no visible global function definition for 'lines'
checkfit.gagafit: no visible global function definition for 'legend'
checkfit.gagafit: no visible global function definition for 'quantile'
checkfit.gagafit: no visible global function definition for 'points'
classpred.gagafit: no visible global function definition for 'is'
findgenes.gagafit: no visible global function definition for 'is'
findgenes.gagafit: no visible global function definition for 'kmeans'
fitGG: no visible global function definition for 'is'
fitGG: no visible global function definition for 'quantile'
fitGG: no visible global function definition for 'var'
fitGG: no visible global function definition for 'kmeans'
fitNN: no visible global function definition for 'is'
fitNNSingleHyp: no visible global function definition for 'is'
forwsimDiffExpr.gagafit: no visible global function definition for 'is'
forwsimDiffExpr.nnfit: no visible global function definition for 'is'
forwsimDiffExpr.nnfit: no visible global function definition for
  'quantile'
makeEBarraysSingleHyp: no visible global function definition for 'new'
parest.gagafit: no visible global function definition for 'is'
parest.gagafit: no visible binding for global variable 'quantile'
parest.gagafit: no visible global function definition for 'quantile'
plotForwSim: no visible global function definition for 'lines'
posmeansGG.gagafit: no visible global function definition for 'is'
powclasspred.gagafit: no visible global function definition for 'is'
powfindgenes.gagafit: no visible global function definition for 'is'
powfindgenes.nnfit: no visible global function definition for 'is'
powfindgenes.nnfit: no visible global function definition for 'sd'
powsimprior.nnfit: no visible global function definition for 'sd'
ppGG: no visible global function definition for 'is'
sigmaPriorEst: no visible global function definition for 'is'
sigmaPriorEst: no visible binding for global variable 'var'
sigmaPriorEst: no visible global function definition for 'var'
simGG: no visible global function definition for 'rgamma'
simGG: no visible global function definition for 'new'
simNN: no visible global function definition for 'runif'
simNN: no visible global function definition for 'rnorm'
simNN: no visible global function definition for 'rgamma'
simNN: no visible global function definition for 'new'
simnewsamples.gagafit: no visible global function definition for 'is'
simnewsamples.gagafit: no visible global function definition for 'new'
simnewsamples.nnfit: no visible global function definition for 'is'
simnewsamples.nnfit: no visible global function definition for 'runif'
simnewsamples.nnfit: no visible global function definition for 'rgamma'
simnewsamples.nnfit: no visible global function definition for 'rnorm'
simnewsamples.nnfit: no visible global function definition for
  'model.matrix'
simnewsamples.nnfit: no visible global function definition for 'new'
Undefined global functions or variables:
  density is kmeans legend lines model.matrix new points predict
  quantile rgamma rnorm runif sd var
Consider adding
  importFrom("graphics", "legend", "lines", "points")
  importFrom("methods", "is", "new")
  importFrom("stats", "density", "kmeans", "model.matrix", "predict",
             "quantile", "rgamma", "rnorm", "runif", "sd", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.19-bioc/R/library/gaga/libs/x64/gaga.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
  'F:/biocbuild/bbs-3.19-bioc/meat/gaga.Rcheck/00check.log'
for details.


Installation output

gaga.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL gaga
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'gaga' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cseqdesma.c -o cseqdesma.o
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cstat.c -o cstat.o
cstat.c: In function 'free_vector':
cstat.c:667:20: warning: the comparison will always evaluate as 'true' for the pointer operand in 'v + (sizetype)((long long unsigned int)nl * 4)' must not be NULL [-Waddress]
  667 |         if( (v+nl) != NULL ) free((char  *) (v+nl));
      |                    ^~
cstat.c: In function 'free_dvector':
cstat.c:673:20: warning: the comparison will always evaluate as 'true' for the pointer operand in 'v + (sizetype)((long long unsigned int)nl * 8)' must not be NULL [-Waddress]
  673 |         if( (v+nl) != NULL ) free((char  *) (v+nl));
      |                    ^~
cstat.c: In function 'free_ivector':
cstat.c:679:20: warning: the comparison will always evaluate as 'true' for the pointer operand in 'v + (sizetype)((long long unsigned int)nl * 4)' must not be NULL [-Waddress]
  679 |         if( (v+nl) != NULL ) free((char  *) (v+nl));
      |                    ^~
cstat.c: In function 'free_dmatrix':
cstat.c:687:47: warning: the comparison will always evaluate as 'true' for the pointer operand in '*(m + (sizetype)((long long unsigned int)i * 8)) + (sizetype)((long long unsigned int)ncl * 8)' must not be NULL [-Waddress]
  687 |         for(i=nrh;i>=nrl;i--) {if( (m[i]+ncl) != NULL )
      |                                               ^~
cstat.c:689:21: warning: the comparison will always evaluate as 'true' for the pointer operand in 'm + (sizetype)((long long unsigned int)nrl * 8)' must not be NULL [-Waddress]
  689 |         if( (m+nrl) != NULL ) free((char  *) (m+nrl));
      |                     ^~
cstat.c: In function 'free_imatrix':
cstat.c:697:47: warning: the comparison will always evaluate as 'true' for the pointer operand in '*(m + (sizetype)((long long unsigned int)i * 8)) + (sizetype)((long long unsigned int)ncl * 4)' must not be NULL [-Waddress]
  697 |         for(i=nrh;i>=nrl;i--) {if( (m[i]+ncl) != NULL )
      |                                               ^~
cstat.c:699:21: warning: the comparison will always evaluate as 'true' for the pointer operand in 'm + (sizetype)((long long unsigned int)nrl * 8)' must not be NULL [-Waddress]
  699 |         if( (m+nrl) != NULL ) free((char  *) (m+nrl));
      |                     ^~
cstat.c: At top level:
cstat.c:22:19: warning: 'css_c_sccs_id' defined but not used [-Wunused-const-variable=]
   22 | static const char css_c_sccs_id[] = "@(#)$Workfile: rand.c$ $Revision: 5$";
      |                   ^~~~~~~~~~~~~
cstat.c:21:19: warning: 'vector_c_sccs_id' defined but not used [-Wunused-const-variable=]
   21 | static const char vector_c_sccs_id[] = "%W%";
      |                   ^~~~~~~~~~~~~~~~
cstat.c:20:19: warning: 'nrutil_c_sccs_id' defined but not used [-Wunused-const-variable=]
   20 | static const char nrutil_c_sccs_id[] = "%W%";
      |                   ^~~~~~~~~~~~~~~~
cstat.c:19:19: warning: 'mess_c_sccs_id' defined but not used [-Wunused-const-variable=]
   19 | static const char mess_c_sccs_id[] = "%W%";
      |                   ^~~~~~~~~~~~~~
cstat.c:18:19: warning: 'interface_c_sccs_id' defined but not used [-Wunused-const-variable=]
   18 | static const char interface_c_sccs_id[] = "%W%";
      |                   ^~~~~~~~~~~~~~~~~~~
cstat.c: In function 'lu_inverse':
cstat.c:1282:4: warning: 'lu_solve' accessing 8 bytes in a region of size 0 [-Wstringop-overflow=]
 1282 |    lu_solve(a,n,indx,col);
      |    ^~~~~~~~~~~~~~~~~~~~~~
cstat.c:1282:4: note: referencing argument 4 of type 'double[0]'
cstat.c:1237:6: note: in a call to function 'lu_solve'
 1237 | void lu_solve(double **a, int n, int *indx, double b[]) {
      |      ^~~~~~~~
In function 'free_dvector',
    inlined from 'dirmin' at cstat.c:4556:2:
cstat.c:673:30: warning: 'free' called on pointer 'xicom' with nonzero offset 8 [-Wfree-nonheap-object]
  673 |         if( (v+nl) != NULL ) free((char  *) (v+nl));
      |                              ^~~~~~~~~~~~~~~~~~~~~~
cstat.c: In function 'dirmin':
cstat.c:4523:15: note: declared here
 4523 | double *pcom,*xicom,(*nrfunc)(double []);
      |               ^~~~~
In function 'free_dvector',
    inlined from 'dirmin' at cstat.c:4557:2:
cstat.c:673:30: warning: 'free' called on pointer 'pcom' with nonzero offset 8 [-Wfree-nonheap-object]
  673 |         if( (v+nl) != NULL ) free((char  *) (v+nl));
      |                              ^~~~~~~~~~~~~~~~~~~~~~
cstat.c: In function 'dirmin':
cstat.c:4523:9: note: declared here
 4523 | double *pcom,*xicom,(*nrfunc)(double []);
      |         ^~~~
cstat.c: In function 'minimize':
cstat.c:4490:7: warning: 'dirmin' accessing 8 bytes in a region of size 0 [-Wstringop-overflow=]
 4490 |       dirmin(th,dirinit,n,fret,f,itmax,eps);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cstat.c:4490:7: note: referencing argument 2 of type 'double[0]'
cstat.c:4525:6: note: in a call to function 'dirmin'
 4525 | void dirmin(double p[], double xi[], int n, double *fret, double (*func)(double []), int itmax, double dirminEPS) {
      |      ^~~~~~
cstat.c:4505:9: warning: 'dirmin' accessing 8 bytes in a region of size 0 [-Wstringop-overflow=]
 4505 |         dirmin(th,dirinit,n,fret,f,itmax,eps);
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cstat.c:4505:9: note: referencing argument 2 of type 'double[0]'
cstat.c:4525:6: note: in a call to function 'dirmin'
 4525 | void dirmin(double p[], double xi[], int n, double *fret, double (*func)(double []), int itmax, double dirminEPS) {
      |      ^~~~~~
gcc -shared -s -static-libgcc -o gaga.dll tmp.def cseqdesma.o cstat.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-gaga/00new/gaga/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (gaga)

Tests output


Example timings

gaga.Rcheck/gaga-Ex.timings

nameusersystemelapsed
buildPatterns000
classpred000
findgenes000
fitGG0.170.000.19
forwsimDiffExpr1.700.011.75
geneclus000
parest000
powfindgenes0.330.000.33
simGG000