Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:07 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 2001/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
snpStats 1.56.0 (landing page) David Clayton
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the snpStats package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/snpStats.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: snpStats |
Version: 1.56.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:snpStats.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings snpStats_1.56.0.tar.gz |
StartedAt: 2024-11-20 02:52:13 -0500 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 02:56:57 -0500 (Wed, 20 Nov 2024) |
EllapsedTime: 284.1 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: snpStats.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:snpStats.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings snpStats_1.56.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/snpStats.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘snpStats/DESCRIPTION’ ... OK * this is package ‘snpStats’ version ‘1.56.0’ * 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 ‘snpStats’ can be installed ... WARNING Found the following significant warnings: bind.c:243:89: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] glm_test_R.c:305:56: warning: data argument not used by format string [-Wformat-extra-args] glm_test_R.c:805:56: warning: data argument not used by format string [-Wformat-extra-args] glm_test_R.c:937:63: warning: data argument not used by format string [-Wformat-extra-args] mvphenotype.c:568:9: warning: variable 'df_rV' is uninitialized when used here [-Wuninitialized] read_uncertain.c:103:62: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] See ‘/Users/biocbuild/bbs-3.20-bioc/meat/snpStats.Rcheck/00install.out’ for details. * used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... NOTE installed size is 5.6Mb sub-directories of 1Mb or more: data 4.1Mb * 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 ... OK * checking Rd files ... NOTE checkRd: (-1) glm.test.control.Rd:28-31: Lost braces in \itemize; meant \describe ? checkRd: (-1) glm.test.control.Rd:32-34: Lost braces in \itemize; meant \describe ? * 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 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 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 ... WARNING Note: information on .o files is not available File ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/snpStats/libs/snpStats.so’: Found ‘___sprintf_chk’, possibly from ‘sprintf’ (C) Found ‘_rand’, possibly from ‘rand’ (C) File ‘snpStats/libs/snpStats.so’: Found non-API call to R: ‘R_data_class’ 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. Compiled code should not call non-API entry points in R. 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: 2 WARNINGs, 2 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/snpStats.Rcheck/00check.log’ for details.
snpStats.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL snpStats ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘snpStats’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Runcertain.c -o Runcertain.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bind.c -o bind.o bind.c:243:89: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] error("Duplicated column name at column %d overall from column %d of object %d", ij+1, j+1, i+1); ~~ ^~~~ %ld 1 warning generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c count_gt.c -o count_gt.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c covwin.c -o covwin.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c force_hom.c -o force_hom.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fst.c -o fst.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c glm_test.c -o glm_test.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c glm_test_R.c -o glm_test_R.o glm_test_R.c:305:56: warning: data argument not used by format string [-Wformat-extra-args] warning("Matrix not positive semi-definite in test ", t+1); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ glm_test_R.c:805:56: warning: data argument not used by format string [-Wformat-extra-args] warning("Matrix not positive semi-definite in test ", test+1); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ glm_test_R.c:368:7: warning: unused variable 'max_name_length' [-Wunused-variable] int max_name_length = MAX_NAME_LENGTH -1; ^ glm_test_R.c:937:63: warning: data argument not used by format string [-Wformat-extra-args] warning("Matrix not positive semi-definite in pooled test ", i+1); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ 4 warnings generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c hash_index.c -o hash_index.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c hphase.c -o hphase.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c imputation.c -o imputation.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c in.c -o in.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c input.c -o input.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c invert.c -o invert.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ipf.c -o ipf.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ld.c -o ld.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c misc.c -o misc.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c mla.c -o mla.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c mvphenotype.c -o mvphenotype.o mvphenotype.c:568:9: warning: variable 'df_rV' is uninitialized when used here [-Wuninitialized] R_Free(df_rV); ^~~~~ /Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:60:46: note: expanded from macro 'R_Free' #define R_Free(p) (R_chk_free( (void *)(p) ), (p) = NULL) ^ mvphenotype.c:486:20: note: initialize the variable 'df_rV' to silence this warning double *df_rV; ^ = NULL 1 warning generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c outdata.c -o outdata.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c plink.c -o plink.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c read_uncertain.c -o read_uncertain.o read_uncertain.c:103:62: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] Rprintf("Reading SnpMatrix with %d rows and %d columns\n", lines, ncol); ~~ ^~~~~ %ld 1 warning generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c readped.c -o readped.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c single_snp_tests.c -o single_snp_tests.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c snp_summary.c -o snp_summary.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c snpmpy.c -o snpmpy.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c solve_cubic.c -o solve_cubic.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c structure.c -o structure.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c subset.c -o subset.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c switch.c -o switch.o switch.c:32:8: warning: variable 'female2' set but not used [-Wunused-but-set-variable] int *female2 = NULL; ^ 1 warning generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c tdt.c -o tdt.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c testBig.c -o testBig.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c uncertain.c -o uncertain.o clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o snpStats.so Runcertain.o bind.o count_gt.o covwin.o force_hom.o fst.o glm_test.o glm_test_R.o hash_index.o hphase.o imputation.o in.o input.o invert.o ipf.o ld.o misc.o mla.o mvphenotype.o outdata.o plink.o read_uncertain.o readped.o single_snp_tests.o snp_summary.o snpmpy.o solve_cubic.o structure.o subset.o switch.o tdt.o testBig.o uncertain.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-snpStats/00new/snpStats/libs ** 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 ** 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 (snpStats)
snpStats.Rcheck/snpStats-Ex.timings
name | user | system | elapsed | |
Fst | 0.376 | 0.023 | 0.400 | |
GlmEstimates-class | 0.001 | 0.001 | 0.001 | |
GlmTests-class | 0.001 | 0.001 | 0.001 | |
ImputationRules-class | 0.000 | 0.001 | 0.001 | |
SingleSnpTests-class | 0.000 | 0.001 | 0.001 | |
SnpMatrix-class | 0.247 | 0.010 | 0.262 | |
XSnpMatrix-class | 0.065 | 0.007 | 0.074 | |
chi.squared | 0.057 | 0.003 | 0.062 | |
families | 0.013 | 0.002 | 0.020 | |
filter.rules | 0 | 0 | 0 | |
for.exercise | 0.732 | 0.015 | 0.752 | |
ibsCount | 0.246 | 0.003 | 0.251 | |
ibsDist | 0.166 | 0.003 | 0.170 | |
imputation.maf | 0.000 | 0.000 | 0.001 | |
impute.snps | 0.472 | 0.018 | 0.491 | |
ld | 0.058 | 0.002 | 0.061 | |
mean2g | 0.058 | 0.003 | 0.062 | |
misinherits | 0.031 | 0.041 | 0.073 | |
mvtests | 0.000 | 0.001 | 0.001 | |
plotUncertainty | 0.000 | 0.001 | 0.000 | |
pool | 0.112 | 0.005 | 0.118 | |
pp | 0.038 | 0.003 | 0.042 | |
qq.chisq | 0 | 0 | 0 | |
random.snps | 0.002 | 0.001 | 0.003 | |
read.beagle | 0 | 0 | 0 | |
read.impute | 0.000 | 0.001 | 0.000 | |
read.long | 0.000 | 0.000 | 0.001 | |
read.mach | 0 | 0 | 0 | |
read.pedfile | 0 | 0 | 0 | |
row.summary | 0.094 | 0.005 | 0.100 | |
single.snp.tests | 0.073 | 0.005 | 0.079 | |
sm.compare | 0.000 | 0.000 | 0.001 | |
snp.cor | 0.297 | 0.004 | 0.303 | |
snp.imputation | 0.468 | 0.012 | 0.480 | |
snp.lhs.estimates | 0.144 | 0.047 | 0.201 | |
snp.lhs.tests | 0.063 | 0.002 | 0.068 | |
snp.pre.multiply | 0.069 | 0.003 | 0.073 | |
snp.rhs.estimates | 0.077 | 0.020 | 0.098 | |
snp.rhs.tests | 0.059 | 0.002 | 0.063 | |
switch.alleles | 0.061 | 0.004 | 0.066 | |
tdt.snp | 0.014 | 0.004 | 0.022 | |
test.allele.switch | 0.085 | 0.006 | 0.093 | |
testdata | 0.095 | 0.006 | 0.103 | |
write.plink | 0.134 | 0.014 | 0.156 | |
xxt | 0.241 | 0.004 | 0.244 | |