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This page was generated on 2016-10-08 19:32:15 -0700 (Sat, 08 Oct 2016).
| Package 144/293 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| IHWpaper 1.0.2 Nikos Ignatiadis
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | ERROR | ||||||
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ ERROR ] | OK |
| Package: IHWpaper |
| Version: 1.0.2 |
| Command: rm -rf IHWpaper.buildbin-libdir IHWpaper.Rcheck && mkdir IHWpaper.buildbin-libdir IHWpaper.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=IHWpaper.buildbin-libdir IHWpaper_1.0.2.tar.gz >IHWpaper.Rcheck\00install.out 2>&1 && cp IHWpaper.Rcheck\00install.out IHWpaper-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=IHWpaper.buildbin-libdir --install="check:IHWpaper-install.out" --force-multiarch --no-vignettes --timings IHWpaper_1.0.2.tar.gz |
| StartedAt: 2016-10-08 12:37:24 -0700 (Sat, 08 Oct 2016) |
| EndedAt: 2016-10-08 12:49:55 -0700 (Sat, 08 Oct 2016) |
| EllapsedTime: 750.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: IHWpaper.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### rm -rf IHWpaper.buildbin-libdir IHWpaper.Rcheck && mkdir IHWpaper.buildbin-libdir IHWpaper.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=IHWpaper.buildbin-libdir IHWpaper_1.0.2.tar.gz >IHWpaper.Rcheck\00install.out 2>&1 && cp IHWpaper.Rcheck\00install.out IHWpaper-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=IHWpaper.buildbin-libdir --install="check:IHWpaper-install.out" --force-multiarch --no-vignettes --timings IHWpaper_1.0.2.tar.gz
###
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* using log directory 'E:/biocbld/bbs-3.3-data-experiment/meat/IHWpaper.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'IHWpaper/DESCRIPTION' ... OK
* this is package 'IHWpaper' version '1.0.2'
* 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 whether package 'IHWpaper' can be installed ... OK
* checking installed package size ... NOTE
installed size is 13.3Mb
sub-directories of 1Mb or more:
doc 1.4Mb
extdata 9.8Mb
libs 1.4Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
scott_fdrreg: no visible global function definition for 'FDRreg'
scott_fdrreg: no visible global function definition for 'getFDR'
sim_fun_eval: no visible binding for global variable 'fdr_method'
sim_fun_eval: no visible binding for global variable 'fdr_pars'
sim_fun_eval: no visible binding for global variable 'FDP'
sim_fun_eval: no visible binding for global variable 'power'
sim_fun_eval: no visible binding for global variable 'rj_ratio'
sim_fun_eval: no visible binding for global variable 'FPR'
sim_fun_eval: no visible global function definition for 'sd'
sim_fun_eval: no visible binding for global variable 'FWER'
Undefined global functions or variables:
FDP FDRreg FPR FWER fdr_method fdr_pars getFDR power rj_ratio sd
Consider adding
importFrom("stats", "power", "sd")
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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'E:/biocbld/bbs-3.3-data-experiment/meat/IHWpaper.buildbin-libdir/IHWpaper/libs/i386/IHWpaper.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
analyze_dataset 10.37 0.05 61.92
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
analyze_dataset 12.61 0.01 35.47
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
Warning message:
running command '"E:/biocbld/BBS-3˜1.3-B/R/bin/i386/R" CMD BATCH --vanilla "testthat.R" "testthat.Rout"' had status 1
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
[1] "TST GBH"
[1] "SBH"
[1] "Clfdr"
[1] "Greedy Indep. Filt."
[1] "IHW"
[1] "IHW-Bonferroni E3"
[1] "Bonferroni"
[1] "qvalue"
Error: incompatible size (20), expecting 2 (the group size) or 1
In addition: There were 47 warnings (use warnings() to see them)
testthat results ================================================================
OK: 0 SKIPPED: 0 FAILED: 0
Execution halted
** running tests for arch 'x64' ...
Running 'testthat.R'
Warning message:
running command '"E:/biocbld/BBS-3˜1.3-B/R/bin/x64/R" CMD BATCH --vanilla "testthat.R" "testthat.Rout"' had status 1
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
[1] "TST GBH"
[1] "SBH"
[1] "Clfdr"
[1] "Greedy Indep. Filt."
[1] "IHW"
[1] "IHW-Bonferroni E3"
[1] "Bonferroni"
[1] "qvalue"
Error: incompatible size (20), expecting 2 (the group size) or 1
In addition: There were 47 warnings (use warnings() to see them)
testthat results ================================================================
OK: 0 SKIPPED: 0 FAILED: 0
Execution halted
* 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: 2 ERRORs, 3 NOTEs
See
'E:/biocbld/bbs-3.3-data-experiment/meat/IHWpaper.Rcheck/00check.log'
for details.
testthat.Rout.fail:
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(IHWpaper)
Loading required package: IHW
>
> test_check("IHWpaper")
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
-- replacing outliers and refitting for 11 genes
-- DESeq argument 'minReplicatesForReplace' = 7
-- original counts are preserved in counts(dds)
estimating dispersions
fitting model and testing
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
[1] "BH"
[1] "LSL GBH"
[1] "TST GBH"
[1] "SBH"
[1] "Clfdr"
[1] "Greedy Indep. Filt."
[1] "IHW"
[1] "IHW-Bonferroni E3"
[1] "Bonferroni"
[1] "qvalue"
Error: incompatible size (20), expecting 2 (the group size) or 1
In addition: There were 47 warnings (use warnings() to see them)
testthat results ================================================================
OK: 0 SKIPPED: 0 FAILED: 0
Execution halted
testthat.Rout.fail:
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(IHWpaper)
Loading required package: IHW
>
> test_check("IHWpaper")
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
-- replacing outliers and refitting for 11 genes
-- DESeq argument 'minReplicatesForReplace' = 7
-- original counts are preserved in counts(dds)
estimating dispersions
fitting model and testing
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
[1] "BH"
[1] "LSL GBH"
[1] "TST GBH"
[1] "SBH"
[1] "Clfdr"
[1] "Greedy Indep. Filt."
[1] "IHW"
[1] "IHW-Bonferroni E3"
[1] "Bonferroni"
[1] "qvalue"
Error: incompatible size (20), expecting 2 (the group size) or 1
In addition: There were 47 warnings (use warnings() to see them)
testthat results ================================================================
OK: 0 SKIPPED: 0 FAILED: 0
Execution halted
IHWpaper.Rcheck/00install.out:
install for i386 * installing *source* package 'IHWpaper' ... ** libs C:/Rtools/mingw_32/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c RcppExports.cpp -o RcppExports.o C:/Rtools/mingw_32/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c ddhf.cpp -o ddhf.o C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o IHWpaper.dll tmp.def RcppExports.o ddhf.o -Lc:/local323/lib/i386 -Lc:/local323/lib -LE:/biocbld/BBS-3˜1.3-B/R/bin/i386 -lR installing to E:/biocbld/bbs-3.3-data-experiment/meat/IHWpaper.buildbin-libdir/IHWpaper/libs/i386 ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded install for x64 * installing *source* package 'IHWpaper' ... ** libs C:/Rtools/mingw_64/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c RcppExports.cpp -o RcppExports.o C:/Rtools/mingw_64/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c ddhf.cpp -o ddhf.o C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o IHWpaper.dll tmp.def RcppExports.o ddhf.o -Lc:/local323/lib/x64 -Lc:/local323/lib -LE:/biocbld/BBS-3˜1.3-B/R/bin/x64 -lR installing to E:/biocbld/bbs-3.3-data-experiment/meat/IHWpaper.buildbin-libdir/IHWpaper/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'IHWpaper' as IHWpaper_1.0.2.zip * DONE (IHWpaper)
IHWpaper.Rcheck/examples_i386/IHWpaper-Ex.timings:
| name | user | system | elapsed | |
| analyze_dataset | 10.37 | 0.05 | 61.92 | |
| bh | 0.07 | 0.01 | 0.17 | |
| bonf | 0.06 | 0.00 | 0.06 | |
| clfdr | 0.20 | 0.00 | 0.21 | |
| continuous_wrap | 0.2 | 0.0 | 0.2 | |
| ddhf | 3.48 | 0.00 | 3.48 | |
| du_ttest_sim | 0.25 | 0.00 | 0.26 | |
| gbh | 0.13 | 0.00 | 0.13 | |
| ihw_naive | 0.28 | 0.00 | 2.08 | |
| lsl_pi0_est | 0.11 | 0.00 | 0.11 | |
| null_sim | 0.02 | 0.00 | 0.01 | |
| pretty_legend | 0.64 | 0.00 | 1.25 | |
| run_evals | 1.95 | 0.02 | 2.45 | |
| storey_qvalue | 0.20 | 0.00 | 0.31 | |
| stratified_bh | 0.12 | 0.00 | 0.13 | |
| tst_pi0_est | 0.06 | 0.00 | 0.06 | |
| wasserman_normal_prds_sim | 0.02 | 0.00 | 0.02 | |
| wasserman_normal_sim | 0.02 | 0.00 | 0.01 | |
IHWpaper.Rcheck/examples_x64/IHWpaper-Ex.timings:
| name | user | system | elapsed | |
| analyze_dataset | 12.61 | 0.01 | 35.47 | |
| bh | 0.07 | 0.00 | 0.08 | |
| bonf | 0.10 | 0.00 | 0.09 | |
| clfdr | 0.29 | 0.00 | 0.30 | |
| continuous_wrap | 0.27 | 0.00 | 0.26 | |
| ddhf | 3.46 | 0.00 | 3.47 | |
| du_ttest_sim | 0.35 | 0.00 | 0.34 | |
| gbh | 0.10 | 0.00 | 0.11 | |
| ihw_naive | 0.22 | 0.00 | 0.54 | |
| lsl_pi0_est | 0.08 | 0.00 | 0.08 | |
| null_sim | 0 | 0 | 0 | |
| pretty_legend | 0.65 | 0.00 | 1.00 | |
| run_evals | 1.90 | 0.00 | 2.54 | |
| storey_qvalue | 0.24 | 0.00 | 0.28 | |
| stratified_bh | 0.11 | 0.00 | 0.11 | |
| tst_pi0_est | 0.08 | 0.00 | 0.08 | |
| wasserman_normal_prds_sim | 0 | 0 | 0 | |
| wasserman_normal_sim | 0.01 | 0.00 | 0.01 | |