| Back to Build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-06-06 11:00:42 -0000 (Tue, 06 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4366 |
| 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 | ||||
|
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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1930/2199 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| snpStats 1.51.0 (landing page) David Clayton
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | |||||||||
| Package: snpStats |
| Version: 1.51.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:snpStats.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings snpStats_1.51.0.tar.gz |
| StartedAt: 2023-06-06 07:18:52 -0000 (Tue, 06 Jun 2023) |
| EndedAt: 2023-06-06 07:22:20 -0000 (Tue, 06 Jun 2023) |
| EllapsedTime: 208.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: snpStats.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:snpStats.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings snpStats_1.51.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/snpStats.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘snpStats/DESCRIPTION’ ... OK
* this is package ‘snpStats’ version ‘1.51.0’
* 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
* used C compiler: ‘gcc (GCC) 10.3.1’
* checking installed package size ... NOTE
installed size is 6.3Mb
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 loading without being on the library search path ... 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 ... 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/R/R-4.3.0/site-library/snpStats/libs/snpStats.so’:
Found ‘rand’, possibly from ‘rand’ (C)
Found ‘sprintf’, possibly from ‘sprintf’ (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 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 ...
‘Fst-vignette.Rnw’... OK
‘data-input-vignette.Rnw’... OK
‘differences.Rnw’... OK
‘imputation-vignette.Rnw’... OK
‘ld-vignette.Rnw’... OK
‘pca-vignette.Rnw’... OK
‘snpStats-vignette.Rnw’... OK
‘tdt-vignette.Rnw’... OK
OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 1 NOTE
See
‘/home/biocbuild/bbs-3.18-bioc/meat/snpStats.Rcheck/00check.log’
for details.
snpStats.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL snpStats ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’ * installing *source* package ‘snpStats’ ... ** using staged installation ** libs using C compiler: ‘gcc (GCC) 10.3.1’ gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c Runcertain.c -o Runcertain.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c bind.c -o bind.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c count_gt.c -o count_gt.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c covwin.c -o covwin.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c force_hom.c -o force_hom.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c fst.c -o fst.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c glm_test.c -o glm_test.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c glm_test_R.c -o glm_test_R.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c hash_index.c -o hash_index.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c hphase.c -o hphase.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c imputation.c -o imputation.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c in.c -o in.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c input.c -o input.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c invert.c -o invert.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c ipf.c -o ipf.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c ld.c -o ld.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c misc.c -o misc.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c mla.c -o mla.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c mvphenotype.c -o mvphenotype.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c outdata.c -o outdata.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c plink.c -o plink.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c read_uncertain.c -o read_uncertain.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c readped.c -o readped.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c single_snp_tests.c -o single_snp_tests.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c snp_summary.c -o snp_summary.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c snpmpy.c -o snpmpy.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c solve_cubic.c -o solve_cubic.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c structure.c -o structure.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c subset.c -o subset.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c switch.c -o switch.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c tdt.c -o tdt.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c testBig.c -o testBig.o gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c uncertain.c -o uncertain.o gcc -shared -L/home/biocbuild/R/R-4.3.0/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/R/R-4.3.0/lib -lR installing to /home/biocbuild/R/R-4.3.0/site-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 | 0.459 | 0.020 | 0.480 | |
| GlmEstimates-class | 0.001 | 0.000 | 0.001 | |
| GlmTests-class | 0.001 | 0.000 | 0.000 | |
| ImputationRules-class | 0 | 0 | 0 | |
| SingleSnpTests-class | 0.000 | 0.000 | 0.001 | |
| SnpMatrix-class | 0.186 | 0.000 | 0.187 | |
| XSnpMatrix-class | 0.085 | 0.000 | 0.086 | |
| chi.squared | 0.067 | 0.003 | 0.069 | |
| families | 0.021 | 0.001 | 0.022 | |
| filter.rules | 0 | 0 | 0 | |
| for.exercise | 1.039 | 0.036 | 1.076 | |
| ibsCount | 0.502 | 0.004 | 0.507 | |
| ibsDist | 0.305 | 0.004 | 0.309 | |
| imputation.maf | 0.000 | 0.000 | 0.001 | |
| impute.snps | 0.582 | 0.008 | 0.591 | |
| ld | 0.07 | 0.00 | 0.07 | |
| mean2g | 0.073 | 0.000 | 0.073 | |
| misinherits | 0.042 | 0.004 | 0.045 | |
| mvtests | 0 | 0 | 0 | |
| plotUncertainty | 0.000 | 0.000 | 0.001 | |
| pool | 0.223 | 0.000 | 0.222 | |
| pp | 0.062 | 0.000 | 0.063 | |
| qq.chisq | 0 | 0 | 0 | |
| random.snps | 0.001 | 0.003 | 0.003 | |
| read.beagle | 0 | 0 | 0 | |
| read.impute | 0.000 | 0.000 | 0.001 | |
| read.long | 0 | 0 | 0 | |
| read.mach | 0 | 0 | 0 | |
| read.pedfile | 0 | 0 | 0 | |
| row.summary | 0.116 | 0.012 | 0.128 | |
| single.snp.tests | 0.095 | 0.004 | 0.098 | |
| sm.compare | 0 | 0 | 0 | |
| snp.cor | 0.541 | 0.000 | 0.541 | |
| snp.imputation | 0.581 | 0.012 | 0.593 | |
| snp.lhs.estimates | 0.220 | 0.000 | 0.221 | |
| snp.lhs.tests | 0.080 | 0.000 | 0.081 | |
| snp.pre.multiply | 0.09 | 0.00 | 0.09 | |
| snp.rhs.estimates | 0.105 | 0.004 | 0.109 | |
| snp.rhs.tests | 0.074 | 0.000 | 0.073 | |
| switch.alleles | 0.078 | 0.000 | 0.077 | |
| tdt.snp | 0.021 | 0.000 | 0.020 | |
| test.allele.switch | 0.112 | 0.004 | 0.116 | |
| testdata | 0.132 | 0.004 | 0.137 | |
| write.plink | 0.119 | 0.000 | 0.119 | |
| xxt | 0.460 | 0.004 | 0.465 | |