David Clayton
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/snpStats |
| Branch: master |
| Last Commit: fdbab4a |
| Last Changed Date: 2018-10-30 11:54:27 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 12:54:41 -0400 (Tue, 09 Apr 2019).
| Package 1523/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| snpStats 1.33.0 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 | OK | [ OK ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: snpStats |
| Version: 1.33.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:snpStats.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings snpStats_1.33.0.tar.gz |
| StartedAt: 2019-04-09 05:39:13 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 05:41:10 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 117.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: snpStats.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:snpStats.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings snpStats_1.33.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/snpStats.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘snpStats/DESCRIPTION’ ... OK
* this is package ‘snpStats’ version ‘1.33.0’
* 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 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 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 ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/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 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 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
‘/Users/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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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL snpStats
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘snpStats’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c Runcertain.c -o Runcertain.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c bind.c -o bind.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c count_gt.c -o count_gt.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c covwin.c -o covwin.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c force_hom.c -o force_hom.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c fst.c -o fst.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c glm_test.c -o glm_test.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c glm_test_R.c -o glm_test_R.o
glm_test_R.c:368:7: warning: unused variable 'max_name_length' [-Wunused-variable]
int max_name_length = MAX_NAME_LENGTH -1;
^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c hash_index.c -o hash_index.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c hphase.c -o hphase.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c imputation.c -o imputation.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c in.c -o in.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c input.c -o input.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c invert.c -o invert.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c ipf.c -o ipf.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c ld.c -o ld.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c misc.c -o misc.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c mla.c -o mla.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c mvphenotype.c -o mvphenotype.o
mvphenotype.c:568:7: warning: variable 'df_rV' is uninitialized when used here [-Wuninitialized]
Free(df_rV);
^˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:74:46: note: expanded from macro 'Free'
#define 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 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c outdata.c -o outdata.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c plink.c -o plink.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c read_uncertain.c -o read_uncertain.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c readped.c -o readped.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c single_snp_tests.c -o single_snp_tests.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c snp_summary.c -o snp_summary.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c snpmpy.c -o snpmpy.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c solve_cubic.c -o solve_cubic.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c structure.c -o structure.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c subset.c -o subset.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c switch.c -o switch.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c tdt.c -o tdt.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c testBig.c -o testBig.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c uncertain.c -o uncertain.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/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 | 0.813 | 0.124 | 0.954 | |
| GlmEstimates-class | 0.002 | 0.000 | 0.002 | |
| GlmTests-class | 0.002 | 0.000 | 0.002 | |
| ImputationRules-class | 0.001 | 0.000 | 0.001 | |
| SingleSnpTests-class | 0.003 | 0.001 | 0.004 | |
| SnpMatrix-class | 0.318 | 0.058 | 0.380 | |
| XSnpMatrix-class | 0.139 | 0.044 | 0.184 | |
| chi.squared | 0.126 | 0.041 | 0.168 | |
| families | 0.038 | 0.034 | 0.072 | |
| filter.rules | 0.001 | 0.000 | 0.000 | |
| for.exercise | 1.355 | 0.048 | 1.403 | |
| ibsCount | 0.728 | 0.053 | 0.783 | |
| ibsDist | 0.401 | 0.043 | 0.444 | |
| imputation.maf | 0.001 | 0.000 | 0.000 | |
| impute.snps | 0.934 | 0.128 | 1.064 | |
| ld | 0.081 | 0.028 | 0.108 | |
| mean2g | 0.082 | 0.028 | 0.110 | |
| misinherits | 0.056 | 0.068 | 0.128 | |
| mvtests | 0.001 | 0.000 | 0.000 | |
| plotUncertainty | 0.000 | 0.001 | 0.000 | |
| pool | 0.204 | 0.049 | 0.252 | |
| pp | 0.088 | 0.005 | 0.092 | |
| qq.chisq | 0.001 | 0.001 | 0.001 | |
| random.snps | 0.004 | 0.001 | 0.005 | |
| read.beagle | 0.001 | 0.000 | 0.000 | |
| read.impute | 0.001 | 0.000 | 0.000 | |
| read.long | 0 | 0 | 0 | |
| read.mach | 0 | 0 | 0 | |
| read.pedfile | 0.000 | 0.001 | 0.001 | |
| row.summary | 0.233 | 0.059 | 0.292 | |
| single.snp.tests | 0.168 | 0.042 | 0.211 | |
| sm.compare | 0.001 | 0.000 | 0.000 | |
| snp.cor | 0.742 | 0.047 | 0.789 | |
| snp.imputation | 0.676 | 0.120 | 0.796 | |
| snp.lhs.estimates | 0.510 | 0.083 | 0.595 | |
| snp.lhs.tests | 0.102 | 0.030 | 0.132 | |
| snp.pre.multiply | 0.147 | 0.036 | 0.184 | |
| snp.rhs.estimates | 0.156 | 0.056 | 0.213 | |
| snp.rhs.tests | 0.121 | 0.044 | 0.164 | |
| switch.alleles | 0.121 | 0.051 | 0.171 | |
| tdt.snp | 0.037 | 0.037 | 0.074 | |
| test.allele.switch | 0.131 | 0.039 | 0.170 | |
| testdata | 0.170 | 0.042 | 0.212 | |
| write.plink | 0.267 | 0.048 | 0.315 | |
| xxt | 0.572 | 0.033 | 0.604 | |