Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-10-17 08:22:19 -0400 (Wed, 17 Oct 2018).
Package 1399/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
snpStats 1.30.0 David Clayton
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: snpStats |
Version: 1.30.0 |
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:snpStats.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings snpStats_1.30.0.tar.gz |
StartedAt: 2018-10-16 03:53:04 -0400 (Tue, 16 Oct 2018) |
EndedAt: 2018-10-16 03:54:00 -0400 (Tue, 16 Oct 2018) |
EllapsedTime: 55.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: snpStats.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:snpStats.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings snpStats_1.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/snpStats.Rcheck’ * using R version 3.5.1 Patched (2018-07-12 r74967) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘snpStats/DESCRIPTION’ ... OK * this is package ‘snpStats’ version ‘1.30.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘snpStats’ can be installed ... OK * checking installed package size ... NOTE installed size is 6.2Mb 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 R 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 mvtests: no visible global function definition for ‘contrasts’ plotUncertainty: no visible global function definition for ‘lines’ plotUncertainty: no visible global function definition for ‘text’ write.plink: no visible global function definition for ‘write.table’ Undefined global functions or variables: contrasts lines text write.table Consider adding importFrom("graphics", "lines", "text") importFrom("stats", "contrasts") importFrom("utils", "write.table") to your NAMESPACE file. * 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 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 compiled code ... NOTE Note: information on .o files is not available File ‘/home/biocbuild/bbs-3.7-bioc/R/library/snpStats/libs/snpStats.so’: 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. 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 files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/home/biocbuild/bbs-3.7-bioc/meat/snpStats.Rcheck/00check.log’ for details.
snpStats.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL snpStats ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’ * installing *source* package ‘snpStats’ ... ** libs gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c Runcertain.c -o Runcertain.o gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c bind.c -o bind.o gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c count_gt.c -o count_gt.o gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c covwin.c -o covwin.o gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c force_hom.c -o force_hom.o gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c fst.c -o fst.o gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c glm_test.c -o glm_test.o gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c glm_test_R.c -o glm_test_R.o glm_test_R.c: In function ‘snp_rhs_score’: glm_test_R.c:368:7: warning: unused variable ‘max_name_length’ [-Wunused-variable] int max_name_length = MAX_NAME_LENGTH -1; ^ gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c hash_index.c -o hash_index.o gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c hphase.c -o hphase.o gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c imputation.c -o imputation.o gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c in.c -o in.o gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c input.c -o input.o gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c invert.c -o invert.o gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c ipf.c -o ipf.o gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c ld.c -o ld.o gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c misc.c -o misc.o gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c mla.c -o mla.o gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c mvphenotype.c -o mvphenotype.o gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c outdata.c -o outdata.o gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c plink.c -o plink.o gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c read_uncertain.c -o read_uncertain.o gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c readped.c -o readped.o gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c single_snp_tests.c -o single_snp_tests.o single_snp_tests.c: In function ‘score_single’: single_snp_tests.c:327:4: warning: ‘name_index’ may be used uninitialized in this function [-Wmaybe-uninitialized] do_impute(Snps, n, diploid, subset, nsubj, name_index, Rule, gt2ht, ^ gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c snp_summary.c -o snp_summary.o gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c snpmpy.c -o snpmpy.o gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c solve_cubic.c -o solve_cubic.o gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c structure.c -o structure.o gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c subset.c -o subset.o gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c switch.c -o switch.o switch.c: In function ‘test_switch’: switch.c:32:8: warning: variable ‘female2’ set but not used [-Wunused-but-set-variable] int *female2 = NULL; ^ gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c tdt.c -o tdt.o gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c testBig.c -o testBig.o gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c uncertain.c -o uncertain.o gcc -shared -L/home/biocbuild/bbs-3.7-bioc/R/lib -L/usr/local/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 -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.7-bioc/R/library/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 * DONE (snpStats)
snpStats.Rcheck/snpStats-Ex.timings
name | user | system | elapsed | |
Fst | 0.592 | 0.036 | 0.651 | |
GlmEstimates-class | 0.000 | 0.000 | 0.001 | |
GlmTests-class | 0.000 | 0.000 | 0.001 | |
ImputationRules-class | 0.000 | 0.000 | 0.001 | |
SingleSnpTests-class | 0.004 | 0.000 | 0.001 | |
SnpMatrix-class | 0.176 | 0.016 | 0.193 | |
XSnpMatrix-class | 0.088 | 0.008 | 0.095 | |
chi.squared | 0.084 | 0.000 | 0.084 | |
families | 0.020 | 0.000 | 0.031 | |
filter.rules | 0.000 | 0.000 | 0.001 | |
for.exercise | 1.056 | 0.024 | 1.081 | |
ibsCount | 0.692 | 0.000 | 0.694 | |
ibsDist | 0.288 | 0.004 | 0.291 | |
imputation.maf | 0.000 | 0.000 | 0.001 | |
impute.snps | 0.584 | 0.024 | 0.608 | |
ld | 0.080 | 0.000 | 0.079 | |
mean2g | 0.072 | 0.008 | 0.080 | |
misinherits | 0.036 | 0.004 | 0.041 | |
mvtests | 0 | 0 | 0 | |
plotUncertainty | 0 | 0 | 0 | |
pool | 0.164 | 0.004 | 0.168 | |
pp | 0.064 | 0.000 | 0.064 | |
qq.chisq | 0 | 0 | 0 | |
random.snps | 0.004 | 0.000 | 0.004 | |
read.beagle | 0.004 | 0.000 | 0.000 | |
read.impute | 0 | 0 | 0 | |
read.long | 0.000 | 0.000 | 0.001 | |
read.mach | 0.000 | 0.000 | 0.001 | |
read.pedfile | 0 | 0 | 0 | |
row.summary | 0.124 | 0.000 | 0.125 | |
single.snp.tests | 0.100 | 0.004 | 0.100 | |
sm.compare | 0.000 | 0.000 | 0.001 | |
snp.cor | 0.420 | 0.008 | 0.428 | |
snp.imputation | 0.620 | 0.016 | 0.637 | |
snp.lhs.estimates | 0.192 | 0.008 | 0.200 | |
snp.lhs.tests | 0.084 | 0.004 | 0.087 | |
snp.pre.multiply | 0.092 | 0.004 | 0.096 | |
snp.rhs.estimates | 0.096 | 0.008 | 0.106 | |
snp.rhs.tests | 0.080 | 0.004 | 0.082 | |
switch.alleles | 0.084 | 0.004 | 0.090 | |
tdt.snp | 0.016 | 0.000 | 0.018 | |
test.allele.switch | 0.100 | 0.000 | 0.102 | |
testdata | 0.128 | 0.004 | 0.131 | |
write.plink | 0.132 | 0.008 | 0.140 | |
xxt | 0.324 | 0.004 | 0.328 | |