Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 763/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
gaga 2.52.0 (landing page) David Rossell
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
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. |
Package: gaga |
Version: 2.52.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:gaga.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings gaga_2.52.0.tar.gz |
StartedAt: 2024-12-20 01:42:21 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 01:43:34 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 72.7 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: gaga.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:gaga.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings gaga_2.52.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/gaga.Rcheck' * using R version 4.4.2 (2024-10-31 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * 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 '2.52.0' * 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-3.20-bioc/meat/gaga.Rcheck/00install.out' for details. * 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 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-3.20-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-3.20-bioc/meat/gaga.Rcheck/00check.log' for details.
gaga.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL gaga ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'gaga' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.3.0' gcc -I"F:/biocbuild/bbs-3.20-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-3.20-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-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-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)
gaga.Rcheck/gaga-Ex.timings
name | user | system | elapsed | |
buildPatterns | 0 | 0 | 0 | |
classpred | 0 | 0 | 0 | |
findgenes | 0 | 0 | 0 | |
fitGG | 0.17 | 0.02 | 0.19 | |
forwsimDiffExpr | 1.83 | 0.00 | 1.83 | |
geneclus | 0 | 0 | 0 | |
parest | 0 | 0 | 0 | |
powfindgenes | 0.31 | 0.00 | 0.31 | |
simGG | 0 | 0 | 0 | |