Xinan Yang
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/seq2pathway |
| Branch: RELEASE_3_7 |
| Last Commit: b5c7433 |
| Last Changed Date: 2018-04-30 10:35:35 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:39:54 -0400 (Wed, 17 Oct 2018).
| Package 1342/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| seq2pathway 1.12.0 Xinan Yang
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: seq2pathway |
| Version: 1.12.0 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:seq2pathway.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings seq2pathway_1.12.0.tar.gz |
| StartedAt: 2018-10-17 04:45:22 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 04:51:36 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 374.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: seq2pathway.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:seq2pathway.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings seq2pathway_1.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/seq2pathway.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.12.0'
* 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'
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 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
data fisher.test gencode_coding head ks.test p.adjust read.table
setTxtProgressBar txtProgressBar write.table
Consider adding
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
FisherTest_GO_BP_MF_CC 2.67 0.06 8.16
runseq2pathway 1.69 0.36 37.19
runseq2gene 0.04 0.00 41.57
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
runseq2pathway 1.34 0.33 41.81
runseq2gene 0.02 0.00 40.06
* 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-3.7-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/3.7/bioc/src/contrib/seq2pathway_1.12.0.tar.gz && rm -rf seq2pathway.buildbin-libdir && mkdir seq2pathway.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=seq2pathway.buildbin-libdir seq2pathway_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL seq2pathway_1.12.0.zip && rm seq2pathway_1.12.0.tar.gz seq2pathway_1.12.0.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
100 1495k 100 1495k 0 0 22.7M 0 --:--:-- --:--:-- --:--:-- 25.1M
install for i386
* installing *source* package 'seq2pathway' ...
** 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
runseq2gene html
runseq2pathway html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'seq2pathway' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'seq2pathway' as seq2pathway_1.12.0.zip
* DONE (seq2pathway)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'seq2pathway' successfully unpacked and MD5 sums checked
In R CMD INSTALL
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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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