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This page was generated on 2024-06-14 14:38 -0400 (Fri, 14 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
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: 2024-06-12 14:00 -0400 (Wed, 12 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


INSTALL 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 INSTALL gaga
StartedAt: 2024-06-12 15:45:26 -0400 (Wed, 12 Jun 2024)
EndedAt: 2024-06-12 15:45:51 -0400 (Wed, 12 Jun 2024)
EllapsedTime: 24.7 seconds
RetCode: 0
Status:   OK  

Command output

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