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This page was generated on 2021-10-15 15:06:04 -0400 (Fri, 15 Oct 2021).
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To the developers/maintainers of the ENVISIONQuery package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ENVISIONQuery.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 578/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ENVISIONQuery 1.40.0 (landing page) Alex Lisovich
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK |  | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| Package: ENVISIONQuery |
| Version: 1.40.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:ENVISIONQuery.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ENVISIONQuery_1.40.0.tar.gz |
| StartedAt: 2021-10-14 22:45:36 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 22:46:20 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 43.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ENVISIONQuery.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:ENVISIONQuery.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ENVISIONQuery_1.40.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/ENVISIONQuery.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ENVISIONQuery/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ENVISIONQuery' version '1.40.0'
* 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:
.BBSoptions
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 'ENVISIONQuery' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
* 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 ... NOTE
Packages in Depends field not imported from:
'XML' 'rJava'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'ENVISIONQuery/R/zzz.R':
.onAttach calls:
cat("This is ", pkgname, " ", desc$Version, " ", desc$Date, "\n")
Package startup functions should use 'packageStartupMessage' to
generate messages.
See section 'Good practice' in '?.onAttach'.
.First.lib: no visible global function definition for 'data'
.onAttach : getJavaVersion: no visible global function definition for
'.jcall'
.onAttach : jpackage: no visible binding for global variable
'.jniInitialized'
.onAttach : jpackage: no visible global function definition for
'.jinit'
.onAttach : jpackage: no visible global function definition for
'.jaddClassPath'
.onAttach : jpackage: no visible global function definition for
'.jaddLibrary'
.onAttach: no visible global function definition for
'packageDescription'
ENVISIONQuery.chunk: no visible global function definition for
'.jarray'
formatIdMap: no visible global function definition for 'xmlTreeParse'
formatIdMap: no visible global function definition for 'xmlRoot'
formatIdMap: no visible global function definition for 'xmlChildren'
formatIntact: no visible global function definition for 'xmlTreeParse'
formatIntact: no visible global function definition for 'xmlRoot'
formatIntact: no visible global function definition for 'xmlChildren'
formatPicr: no visible global function definition for 'xmlTreeParse'
formatPicr: no visible global function definition for 'xmlRoot'
formatPicr: no visible global function definition for 'xmlChildren'
formatReactome: no visible global function definition for
'xmlTreeParse'
formatReactome: no visible global function definition for 'xmlRoot'
formatReactome: no visible global function definition for 'xmlChildren'
getIdEntries: no visible global function definition for 'xmlChildren'
getIdEntries : <anonymous>: no visible global function definition for
'xmlAttrs'
getIdMatchInfo: no visible global function definition for 'xmlChildren'
getIdMatchInfo : <anonymous>: no visible global function definition for
'xmlAttrs'
getIdMatchInfo : <anonymous>: no visible global function definition for
'xmlValue'
getIdMatchInfo : <anonymous>: no visible global function definition for
'xmlChildren'
getInputIdEntries: no visible global function definition for
'xmlChildren'
getInputIdEntries : <anonymous>: no visible global function definition
for 'xmlAttrs'
getIntactMatchInfo: no visible global function definition for
'xmlChildren'
getIntactMatchInfo : <anonymous>: no visible global function definition
for 'xmlAttrs'
getIntactMatchInfo: no visible global function definition for
'xmlAttrs'
getPicrMatchInfo: no visible global function definition for
'xmlChildren'
getPicrMatchInfo : <anonymous>: no visible global function definition
for 'xmlAttrs'
getPicrMatchInfo: no visible global function definition for 'xmlAttrs'
getPositiveResultSetIDs: no visible global function definition for
'xmlChildren'
getPositiveResultSetIDs: no visible global function definition for
'xmlAttrs'
getPositiveResultSetIDs : <anonymous>: no visible global function
definition for 'xmlAttrs'
getReactomeMatchInfo: no visible global function definition for
'xmlChildren'
getReactomeMatchInfo : <anonymous>: no visible global function
definition for 'xmlAttrs'
getReactomeMatchInfo: no visible global function definition for
'xmlValue'
getReactomeMatchInfo: no visible global function definition for
'xmlAttrs'
getService: no visible global function definition for 'menu'
getServices: no visible global function definition for
'assignInNamespace'
getTool: no visible global function definition for 'menu'
progressMsg: no visible global function definition for 'flush.console'
registerServices: no visible global function definition for 'new'
registerServices: no visible global function definition for 'J'
Undefined global functions or variables:
.jaddClassPath .jaddLibrary .jarray .jcall .jinit .jniInitialized J
assignInNamespace data flush.console menu new packageDescription
xmlAttrs xmlChildren xmlRoot xmlTreeParse xmlValue
Consider adding
importFrom("methods", "new")
importFrom("utils", "assignInNamespace", "data", "flush.console",
"menu", "packageDescription")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 files in 'vignettes' ... OK
* checking examples ... OK
* 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: 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/ENVISIONQuery.Rcheck/00check.log'
for details.
ENVISIONQuery.Rcheck/00install.out
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch ENVISIONQuery
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* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
* installing *source* package 'ENVISIONQuery' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'ENVISIONQuery'
finding HTML links ... done
ENVISIONQuery-package html
ENVISIONQuery html
ENVISIONQuery.chunk html
ENVISIONQuery.loop html
ENVISIONServices html
formatIdMap html
formatIntact html
formatPicr html
formatReactome html
getFormatter html
getIdEntries html
getIdMatchInfo html
getInputIdEntries html
getInputTypes html
getIntactMatchInfo html
getMerger html
getPicrMatchInfo html
getPositiveResultSetIDs html
getReactomeMatchInfo html
getService html
getServiceClient html
getServiceNames html
getServiceOptions html
getServices html
getTool html
getToolNames html
jgetOptions html
mergeFrameList html
mergeMatchRows html
progressMsg html
registerServices html
toChunks html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
This is ENVISIONQuery 1.40.0 2020-09-01
** testing if installed package can be loaded from final location
This is ENVISIONQuery 1.40.0 2020-09-01
** testing if installed package keeps a record of temporary installation path
* DONE (ENVISIONQuery)
Making 'packages.html' ... done
ENVISIONQuery.Rcheck/ENVISIONQuery-Ex.timings
| name | user | system | elapsed | |
| ENVISIONQuery | 1.83 | 0.19 | 2.20 | |
| getInputTypes | 0 | 0 | 0 | |
| getService | 0 | 0 | 0 | |
| getServiceClient | 0 | 0 | 0 | |
| getServiceNames | 0 | 0 | 0 | |
| getServiceOptions | 0.01 | 0.00 | 0.02 | |
| getServices | 0 | 0 | 0 | |
| getTool | 0 | 0 | 0 | |
| getToolNames | 0 | 0 | 0 | |