Xinan Yang
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/seq2pathway |
| Branch: RELEASE_3_9 |
| Last Commit: acd43f5 |
| Last Changed Date: 2019-05-02 11:53:52 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:32:20 -0400 (Wed, 16 Oct 2019).
| Package 1489/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| seq2pathway 1.16.0 Xinan Yang
| 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 | |
| Package: seq2pathway |
| Version: 1.16.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:seq2pathway.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings seq2pathway_1.16.0.tar.gz |
| StartedAt: 2019-10-16 07:00:38 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 07:07:06 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 387.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: seq2pathway.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:seq2pathway.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings seq2pathway_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/seq2pathway.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'seq2pathway/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'seq2pathway' version '1.16.0'
* 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 whether package 'seq2pathway' can be installed ... OK
* checking installed package size ... OK
* 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
* 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 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
FAIME_EmpiricalP: no visible global function definition for 'data'
FAIME_EmpiricalP: no visible binding for global variable
'gencode_coding'
FisherTest_GO_BP_MF_CC: no visible global function definition for
'data'
FisherTest_GO_BP_MF_CC: no visible binding for global variable
'GO_BP_list'
FisherTest_GO_BP_MF_CC: no visible binding for global variable
'GO_MF_list'
FisherTest_GO_BP_MF_CC: no visible binding for global variable
'GO_CC_list'
FisherTest_GO_BP_MF_CC: no visible binding for global variable
'Des_BP_list'
FisherTest_GO_BP_MF_CC: no visible binding for global variable
'Des_MF_list'
FisherTest_GO_BP_MF_CC: no visible binding for global variable
'Des_CC_list'
FisherTest_GO_BP_MF_CC: no visible binding for global variable
'GO_GENCODE_df_hg_v20'
FisherTest_GO_BP_MF_CC: no visible binding for global variable
'GO_GENCODE_df_hg_v19'
FisherTest_GO_BP_MF_CC: no visible binding for global variable
'GO_GENCODE_df_mm_vM4'
FisherTest_GO_BP_MF_CC: no visible binding for global variable
'GO_GENCODE_df_mm_vM1'
FisherTest_GO_BP_MF_CC: no visible global function definition for
'fisher.test'
FisherTest_GO_BP_MF_CC: no visible global function definition for
'p.adjust'
FisherTest_MsigDB: no visible global function definition for 'data'
FisherTest_MsigDB: no visible binding for global variable
'Msig_GENCODE_df_hg_v20'
FisherTest_MsigDB: no visible binding for global variable
'Msig_GENCODE_df_hg_v19'
FisherTest_MsigDB: no visible binding for global variable
'Msig_GENCODE_df_mm_vM4'
FisherTest_MsigDB: no visible binding for global variable
'Msig_GENCODE_df_mm_vM1'
FisherTest_MsigDB: no visible global function definition for
'fisher.test'
FisherTest_MsigDB: no visible global function definition for 'p.adjust'
KSrank: no visible global function definition for 'ks.test'
KSrank_EmpiricalP: no visible global function definition for 'data'
KSrank_EmpiricalP: no visible binding for global variable
'gencode_coding'
KSrank_EmpiricalP: no visible global function definition for 'ks.test'
Normalize_F: no visible global function definition for 'head'
cumulativerank_EmpiricalP: no visible global function definition for
'data'
cumulativerank_EmpiricalP: no visible binding for global variable
'gencode_coding'
gene2pathway_test: no visible global function definition for 'data'
gene2pathway_test: no visible binding for global variable 'GO_BP_list'
gene2pathway_test: no visible binding for global variable 'GO_MF_list'
gene2pathway_test: no visible binding for global variable 'GO_CC_list'
gene2pathway_test: no visible binding for global variable 'Des_BP_list'
gene2pathway_test: no visible binding for global variable 'Des_CC_list'
gene2pathway_test: no visible binding for global variable 'Des_MF_list'
plotTop10: no visible binding for global variable 'Fisher_odds'
plotTop10: no visible binding for global variable 'FDR'
plotTop10: no visible global function definition for 'barplot'
plotTop10: no visible global function definition for 'lines'
plotTop10: no visible global function definition for 'text'
plotTop10: no visible global function definition for 'abline'
rungene2pathway_EmpiricalP: no visible global function definition for
'txtProgressBar'
rungene2pathway_EmpiricalP: no visible global function definition for
'setTxtProgressBar'
runseq2gene: no visible global function definition for 'write.table'
runseq2gene: no visible global function definition for 'read.table'
runseq2pathway: no visible global function definition for 'data'
runseq2pathway: no visible binding for global variable 'GO_BP_list'
runseq2pathway: no visible binding for global variable 'GO_MF_list'
runseq2pathway: no visible binding for global variable 'GO_CC_list'
runseq2pathway: no visible binding for global variable 'Des_BP_list'
runseq2pathway: no visible binding for global variable 'Des_CC_list'
runseq2pathway: no visible binding for global variable 'Des_MF_list'
runseq2pathway: no visible global function definition for 'write.table'
runseq2pathway: no visible global function definition for 'read.table'
Undefined global functions or variables:
Des_BP_list Des_CC_list Des_MF_list FDR Fisher_odds GO_BP_list
GO_CC_list GO_GENCODE_df_hg_v19 GO_GENCODE_df_hg_v20
GO_GENCODE_df_mm_vM1 GO_GENCODE_df_mm_vM4 GO_MF_list
Msig_GENCODE_df_hg_v19 Msig_GENCODE_df_hg_v20 Msig_GENCODE_df_mm_vM1
Msig_GENCODE_df_mm_vM4 abline barplot data fisher.test gencode_coding
head ks.test lines p.adjust read.table setTxtProgressBar text
txtProgressBar write.table
Consider adding
importFrom("graphics", "abline", "barplot", "lines", "text")
importFrom("stats", "fisher.test", "ks.test", "p.adjust")
importFrom("utils", "data", "head", "read.table", "setTxtProgressBar",
"txtProgressBar", "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 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
runseq2pathway 1.82 0.36 37.39
runseq2gene 0.00 0.02 48.80
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
runseq2pathway 1.53 0.24 35.03
runseq2gene 0.00 0.00 42.23
* 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: 1 NOTE
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/seq2pathway.Rcheck/00check.log'
for details.
seq2pathway.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/seq2pathway_1.16.0.tar.gz && rm -rf seq2pathway.buildbin-libdir && mkdir seq2pathway.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=seq2pathway.buildbin-libdir seq2pathway_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL seq2pathway_1.16.0.zip && rm seq2pathway_1.16.0.tar.gz seq2pathway_1.16.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 11.0M 100 11.0M 0 0 24.4M 0 --:--:-- --:--:-- --:--:-- 24.7M
install for i386
* installing *source* package 'seq2pathway' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'seq2pathway'
finding HTML links ... done
Chipseq_Peak_demo html
FisherTest_GO_BP_MF_CC html
FisherTest_MsigDB html
GRanges_demo html
addDescription html
dat_RNA html
dat_chip html
gene2pathway_test html
plotTop10 html
runseq2gene html
runseq2pathway html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'seq2pathway' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'seq2pathway' as seq2pathway_1.16.0.zip
* DONE (seq2pathway)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'seq2pathway' successfully unpacked and MD5 sums checked
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seq2pathway.Rcheck/examples_i386/seq2pathway-Ex.timings
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seq2pathway.Rcheck/examples_x64/seq2pathway-Ex.timings
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