David Clayton
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/snpStats |
| Branch: RELEASE_3_9 |
| Last Commit: e31cdfb |
| Last Changed Date: 2019-05-02 11:53:09 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 11:56:48 -0400 (Wed, 16 Oct 2019).
| Package 1553/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| snpStats 1.34.0 David Clayton
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | ERROR | skipped | skipped |
| Package: snpStats |
| Version: 1.34.0 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:snpStats.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings snpStats_1.34.0.tar.gz |
| StartedAt: 2019-10-16 05:09:28 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 05:10:49 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 80.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: snpStats.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:snpStats.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings snpStats_1.34.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/snpStats.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.34.0’
* 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-3.9-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-3.9-bioc/meat/snpStats.Rcheck/00check.log’
for details.
snpStats.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL snpStats
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘snpStats’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c Runcertain.c -o Runcertain.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c bind.c -o bind.o
gcc -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c covwin.c -o covwin.o
gcc -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c fst.c -o fst.o
gcc -I"/home/biocbuild/bbs-3.9-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-3.9-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-3.9-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-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c hphase.c -o hphase.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c imputation.c -o imputation.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c in.c -o in.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c input.c -o input.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c invert.c -o invert.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c ipf.c -o ipf.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c ld.c -o ld.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c misc.c -o misc.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c mla.c -o mla.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c mvphenotype.c -o mvphenotype.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c outdata.c -o outdata.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c plink.c -o plink.o
gcc -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c readped.c -o readped.o
gcc -I"/home/biocbuild/bbs-3.9-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:223:4: warning: ‘name_index’ may be used uninitialized in this function [-Wmaybe-uninitialized]
do_impute(Snps, n, NULL, subset, nsubj, name_index, Rule, gt2ht,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
xadd, xdom);
~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c snpmpy.c -o snpmpy.o
gcc -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c structure.c -o structure.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c subset.c -o subset.o
gcc -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c tdt.c -o tdt.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c testBig.c -o testBig.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c uncertain.c -o uncertain.o
gcc -shared -L/home/biocbuild/bbs-3.9-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-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/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 | 0.646 | 0.044 | 0.698 | |
| GlmEstimates-class | 0.001 | 0.000 | 0.001 | |
| GlmTests-class | 0.001 | 0.000 | 0.001 | |
| ImputationRules-class | 0 | 0 | 0 | |
| SingleSnpTests-class | 0 | 0 | 0 | |
| SnpMatrix-class | 0.174 | 0.015 | 0.189 | |
| XSnpMatrix-class | 0.089 | 0.004 | 0.093 | |
| chi.squared | 0.073 | 0.004 | 0.077 | |
| families | 0.018 | 0.000 | 0.019 | |
| filter.rules | 0 | 0 | 0 | |
| for.exercise | 0.922 | 0.004 | 0.926 | |
| ibsCount | 0.971 | 0.004 | 0.975 | |
| ibsDist | 0.505 | 0.000 | 0.505 | |
| imputation.maf | 0.001 | 0.000 | 0.001 | |
| impute.snps | 0.848 | 0.028 | 0.876 | |
| ld | 0.116 | 0.000 | 0.116 | |
| mean2g | 0.125 | 0.004 | 0.129 | |
| misinherits | 0.058 | 0.004 | 0.062 | |
| mvtests | 0 | 0 | 0 | |
| plotUncertainty | 0 | 0 | 0 | |
| pool | 0.247 | 0.008 | 0.255 | |
| pp | 0.109 | 0.001 | 0.127 | |
| qq.chisq | 0 | 0 | 0 | |
| random.snps | 0.004 | 0.001 | 0.005 | |
| read.beagle | 0 | 0 | 0 | |
| read.impute | 0 | 0 | 0 | |
| read.long | 0 | 0 | 0 | |
| read.mach | 0 | 0 | 0 | |
| read.pedfile | 0 | 0 | 0 | |
| row.summary | 0.184 | 0.012 | 0.196 | |
| single.snp.tests | 0.145 | 0.004 | 0.149 | |
| sm.compare | 0.000 | 0.001 | 0.000 | |
| snp.cor | 0.684 | 0.007 | 0.691 | |
| snp.imputation | 0.604 | 0.035 | 0.641 | |
| snp.lhs.estimates | 0.502 | 0.020 | 0.523 | |
| snp.lhs.tests | 0.114 | 0.000 | 0.114 | |
| snp.pre.multiply | 0.090 | 0.004 | 0.094 | |
| snp.rhs.estimates | 0.096 | 0.016 | 0.112 | |
| snp.rhs.tests | 0.074 | 0.008 | 0.082 | |
| switch.alleles | 0.101 | 0.008 | 0.108 | |
| tdt.snp | 0.010 | 0.007 | 0.018 | |
| test.allele.switch | 0.113 | 0.004 | 0.117 | |
| testdata | 0.148 | 0.000 | 0.149 | |
| write.plink | 0.138 | 0.004 | 0.142 | |
| xxt | 0.43 | 0.00 | 0.43 | |