| Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:07:20 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
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To the developers/maintainers of the seq2pathway package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/seq2pathway.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1761/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| seq2pathway 1.26.0 (landing page) Arjun Kinstlick
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: seq2pathway |
| Version: 1.26.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:seq2pathway.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings seq2pathway_1.26.0.tar.gz |
| StartedAt: 2022-04-13 02:44:27 -0400 (Wed, 13 Apr 2022) |
| EndedAt: 2022-04-13 02:50:47 -0400 (Wed, 13 Apr 2022) |
| EllapsedTime: 380.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: seq2pathway.Rcheck |
| Warnings: 2 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:seq2pathway.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings seq2pathway_1.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/seq2pathway.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '1.26.0'
* 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 ... NOTE
Found the following hidden files and directories:
vignettes/.RData
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'seq2pathway' can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import 'WGCNA::cor' by 'stats::cor' when loading 'seq2pathway'
See 'C:/Users/biocbuild/bbs-3.14-bioc/meat/seq2pathway.Rcheck/00install.out' for details.
* 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 ... NOTE
Found the following CITATION file in a non-standard place:
CITATION
Most likely 'inst/CITATION' should be used instead.
* 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 ... WARNING
'library' or 'require' call not declared from: 'biomaRt'
'library' or 'require' call to 'biomaRt' in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* 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_v36'
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_vM25'
FisherTest_GO_BP_MF_CC: no visible binding for global variable
'GO_GENCODE_df_mm_vM1'
FisherTest_MsigDB: no visible global function definition for 'data'
FisherTest_MsigDB: no visible binding for global variable
'Msig_GENCODE_df_hg_v36'
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_vM25'
FisherTest_MsigDB: no visible binding for global variable
'Msig_GENCODE_df_mm_vM1'
KSrank_EmpiricalP: no visible global function definition for 'data'
KSrank_EmpiricalP: no visible binding for global variable
'gencode_coding'
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_v36
GO_GENCODE_df_mm_vM1 GO_GENCODE_df_mm_vM25 GO_MF_list
Msig_GENCODE_df_hg_v19 Msig_GENCODE_df_hg_v36 Msig_GENCODE_df_mm_vM1
Msig_GENCODE_df_mm_vM25 abline barplot data gencode_coding head lines
read.table setTxtProgressBar text txtProgressBar write.table
Consider adding
importFrom("graphics", "abline", "barplot", "lines", "text")
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 (user + system) or elapsed time > 5s
user system elapsed
addDescription 4.20 0.03 5.40
runseq2pathway 1.57 0.09 34.39
runseq2gene 0.01 0.00 38.84
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
runseq2pathway 1.28 0.08 30.25
runseq2gene 0.00 0.01 32.61
* 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 WARNINGs, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.14-bioc/meat/seq2pathway.Rcheck/00check.log'
for details.
seq2pathway.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/seq2pathway_1.26.0.tar.gz && rm -rf seq2pathway.buildbin-libdir && mkdir seq2pathway.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=seq2pathway.buildbin-libdir seq2pathway_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL seq2pathway_1.26.0.zip && rm seq2pathway_1.26.0.tar.gz seq2pathway_1.26.0.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 816k 100 816k 0 0 868k 0 --:--:-- --:--:-- --:--:-- 868k
100 816k 100 816k 0 0 868k 0 --:--:-- --:--:-- --:--:-- 868k
install for i386
* installing *source* package 'seq2pathway' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'WGCNA::cor' by 'stats::cor' when loading 'seq2pathway'
** 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
Warning: replacing previous import 'WGCNA::cor' by 'stats::cor' when loading 'seq2pathway'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'WGCNA::cor' by 'stats::cor' when loading 'seq2pathway'
** 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
Warning: replacing previous import 'WGCNA::cor' by 'stats::cor' when loading 'seq2pathway'
* MD5 sums
packaged installation of 'seq2pathway' as seq2pathway_1.26.0.zip
* DONE (seq2pathway)
* installing to library 'C:/Users/biocbuild/bbs-3.14-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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