Arjun Kinstlick
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/seq2pathway |
| git_branch: master |
| git_last_commit: d41c10b |
| git_last_commit_date: 2021-11-21 00:53:43 -0400 (Sun, 21 Nov 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:40 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1769/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| seq2pathway 1.27.1 (landing page) Arjun Kinstlick
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: seq2pathway |
| Version: 1.27.1 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:seq2pathway.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings seq2pathway_1.27.1.tar.gz |
| StartedAt: 2022-03-17 20:14:59 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 20:18:36 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 216.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: seq2pathway.Rcheck |
| Warnings: 2 |
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### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:seq2pathway.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings seq2pathway_1.27.1.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/seq2pathway.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '1.27.1'
* 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 'D:/biocbuild/bbs-3.15-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
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
runseq2pathway 0.96 0.08 20.34
runseq2gene 0.03 0.01 19.61
* 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
'D:/biocbuild/bbs-3.15-bioc/meat/seq2pathway.Rcheck/00check.log'
for details.
seq2pathway.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL seq2pathway
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* 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
* DONE (seq2pathway)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'TarSeqQC' is missing or broken
done
seq2pathway.Rcheck/seq2pathway-Ex.timings
| name | user | system | elapsed | |
| Chipseq_Peak_demo | 0 | 0 | 0 | |
| FisherTest_GO_BP_MF_CC | 2.79 | 0.06 | 2.86 | |
| FisherTest_MsigDB | 1.66 | 0.06 | 1.75 | |
| GRanges_demo | 0 | 0 | 0 | |
| addDescription | 1.59 | 0.05 | 3.12 | |
| dat_RNA | 0 | 0 | 0 | |
| dat_chip | 0.00 | 0.02 | 0.02 | |
| gene2pathway_test | 0.38 | 0.00 | 0.37 | |
| plotTop10 | 2.12 | 0.36 | 2.49 | |
| runseq2gene | 0.03 | 0.01 | 19.61 | |
| runseq2pathway | 0.96 | 0.08 | 20.34 | |