InterMine Team
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/InterMineR |
| Branch: RELEASE_3_12 |
| Last Commit: ecd9a83 |
| Last Changed Date: 2021-04-28 05:11:58 -0400 (Wed, 28 Apr 2021) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:28:01 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the InterMineR package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 905/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| InterMineR 1.12.3 (landing page) InterMine Team
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: InterMineR |
| Version: 1.12.3 |
| Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:InterMineR.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings InterMineR_1.12.3.tar.gz |
| StartedAt: 2021-05-06 02:42:04 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 02:45:53 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 228.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: InterMineR.Rcheck |
| Warnings: 7 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:InterMineR.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings InterMineR_1.12.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/InterMineR.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘InterMineR/DESCRIPTION’ ... OK
* this is package ‘InterMineR’ version ‘1.12.3’
* 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:
.travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘InterMineR’ can be installed ... WARNING
Found the following significant warnings:
Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:41: unexpected section header '\arguments'
Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:42: unknown macro '\item'
Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:50: unexpected section header '\arguments'
Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:51: unknown macro '\item'
Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:59: unexpected section header '\arguments'
Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:60: unknown macro '\item'
Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:63: unknown macro '\item'
Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:66: unknown macro '\item'
Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:69: unknown macro '\item'
Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:72: unknown macro '\item'
Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:80: unexpected section header '\arguments'
Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:81: unknown macro '\item'
Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:84: unknown macro '\item'
Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:87: unknown macro '\item'
Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:90: unknown macro '\item'
Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:98: unexpected section header '\arguments'
Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:99: unknown macro '\item'
Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:102: unknown macro '\item'
Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:105: unknown macro '\item'
Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:108: unknown macro '\item'
Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:116: unexpected section header '\arguments'
Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:117: unknown macro '\item'
Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:120: unknown macro '\item'
Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:123: unknown macro '\item'
Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:126: unknown macro '\item'
Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:134: unexpected section header '\arguments'
Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:135: unknown macro '\item'
Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:138: unknown macro '\item'
Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:141: unknown macro '\item'
Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:144: unknown macro '\item'
Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:147: unknown macro '\item'
Warning: multiple methods tables found for ‘union’
Warning: multiple methods tables found for ‘intersect’
See ‘/home/biocbuild/bbs-3.12-bioc/meat/InterMineR.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 ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... WARNING
Invalid citation information in ‘inst/CITATION’:
Error in tools:::.parse_CITATION_file(file, meta$Encoding): non-ASCII input in a CITATION file without a declared encoding
* 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 ... NOTE
Warning: multiple methods tables found for ‘union’
Warning: multiple methods tables found for ‘intersect’
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* 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
convertToGeneAnswers: no visible binding for global variable
‘geneExpProfile’
convertToRangedSummarizedExperiment: no visible global function
definition for ‘reshape’
listDatasets: no visible binding for global variable ‘child_name’
create_list,ListManager: no visible global function definition for
‘URLencode’
doEnrichment,Service: no visible global function definition for
‘URLencode’
do_operation,ListManager: no visible global function definition for
‘URLencode’
runQuery,ANY-InterMineR: no visible global function definition for
‘URLencode’
runQuery,ANY-list: no visible global function definition for
‘URLencode’
subtract,ListManager: no visible global function definition for
‘URLencode’
Undefined global functions or variables:
URLencode child_name geneExpProfile reshape
Consider adding
importFrom("stats", "reshape")
importFrom("utils", "URLencode")
to your NAMESPACE file.
* checking Rd files ... WARNING
prepare_Rd: man/ListManager-methods.Rd:41: unexpected section header '\arguments'
prepare_Rd: man/ListManager-methods.Rd:42: unknown macro '\item'
prepare_Rd: man/ListManager-methods.Rd:50: unexpected section header '\arguments'
prepare_Rd: man/ListManager-methods.Rd:51: unknown macro '\item'
prepare_Rd: man/ListManager-methods.Rd:59: unexpected section header '\arguments'
prepare_Rd: man/ListManager-methods.Rd:60: unknown macro '\item'
prepare_Rd: man/ListManager-methods.Rd:63: unknown macro '\item'
prepare_Rd: man/ListManager-methods.Rd:66: unknown macro '\item'
prepare_Rd: man/ListManager-methods.Rd:69: unknown macro '\item'
prepare_Rd: man/ListManager-methods.Rd:72: unknown macro '\item'
prepare_Rd: man/ListManager-methods.Rd:80: unexpected section header '\arguments'
prepare_Rd: man/ListManager-methods.Rd:81: unknown macro '\item'
prepare_Rd: man/ListManager-methods.Rd:84: unknown macro '\item'
prepare_Rd: man/ListManager-methods.Rd:87: unknown macro '\item'
prepare_Rd: man/ListManager-methods.Rd:90: unknown macro '\item'
prepare_Rd: man/ListManager-methods.Rd:98: unexpected section header '\arguments'
prepare_Rd: man/ListManager-methods.Rd:99: unknown macro '\item'
prepare_Rd: man/ListManager-methods.Rd:102: unknown macro '\item'
prepare_Rd: man/ListManager-methods.Rd:105: unknown macro '\item'
prepare_Rd: man/ListManager-methods.Rd:108: unknown macro '\item'
prepare_Rd: man/ListManager-methods.Rd:116: unexpected section header '\arguments'
prepare_Rd: man/ListManager-methods.Rd:117: unknown macro '\item'
prepare_Rd: man/ListManager-methods.Rd:120: unknown macro '\item'
prepare_Rd: man/ListManager-methods.Rd:123: unknown macro '\item'
prepare_Rd: man/ListManager-methods.Rd:126: unknown macro '\item'
prepare_Rd: man/ListManager-methods.Rd:134: unexpected section header '\arguments'
prepare_Rd: man/ListManager-methods.Rd:135: unknown macro '\item'
prepare_Rd: man/ListManager-methods.Rd:138: unknown macro '\item'
prepare_Rd: man/ListManager-methods.Rd:141: unknown macro '\item'
prepare_Rd: man/ListManager-methods.Rd:144: unknown macro '\item'
prepare_Rd: man/ListManager-methods.Rd:147: unknown macro '\item'
* checking Rd metadata ... WARNING
Rd files with duplicated alias 'webservice-methods':
‘doEnrichment.Rd’ ‘list_manager.Rd’
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘GET_api_list’ ‘get_unused_list_name’
Undocumented S4 classes:
‘Service’
Undocumented S4 methods:
generic 'GET_api_list' and siglist 'ListManager'
generic 'doEnrichment' and siglist 'Service'
generic 'get_unused_list_name' and siglist 'ListManager'
generic 'list_manager' and siglist 'Service'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'doEnrichment':
doEnrichment
Code: function(object, ...)
Docs: function(- Service class, genelist = NULL, ids = NULL, widget =
NULL, population = NULL, maxp = 0.05, correction =
"Benjamini Hochberg", filter = NULL, organism = NULL)
Argument names in code not in docs:
object ...
Argument names in docs not in code:
- Service class genelist ids widget population maxp correction
filter organism
Mismatches in argument names:
Position: 1 Code: object Docs: - Service class
Position: 2 Code: ... Docs: genelist
Codoc mismatches from documentation object 'list_manager':
list_manager
Code: function(object, ...)
Docs: function(- Service class)
Argument names in code not in docs:
object ...
Argument names in docs not in code:
- Service class
Mismatches in argument names:
Position: 1 Code: object Docs: - Service class
S4 class codoc mismatches from documentation object 'ListManager-class':
Slots for class 'ListManager'
Code: DEFAULT_DESCRIPTION DEFAULT_LIST_NAME DIFFERENCE_PATH
INTERSECTION_PATH LIST_PATH SUBTRACTION_PATH UNION_PATH mine
token
Docs: DEFAULT_DESCRIPTION DEFAULT_LIST_NAME DIFFERENCE_PATH
INTERSECTION_PATH LIST_PATH SUBTRACTION_PATH UNION_PATH mine
name token
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'doEnrichment'
‘Service - class’
Documented arguments not in \usage in documentation object 'doEnrichment':
‘Service-class’
Undocumented arguments in documentation object 'list_manager'
‘Service - class’
Documented arguments not in \usage in documentation object 'list_manager':
‘Service-class’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
simplifyResult 11.396 0.024 14.034
convertToRangedSummarizedExperiment 4.576 0.032 9.057
runQuery 4.176 0.012 7.443
* 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: 7 WARNINGs, 4 NOTEs
See
‘/home/biocbuild/bbs-3.12-bioc/meat/InterMineR.Rcheck/00check.log’
for details.
InterMineR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL InterMineR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’ * installing *source* package ‘InterMineR’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘intersect’ in package ‘InterMineR’ Creating a new generic function for ‘union’ in package ‘InterMineR’ ** help Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:41: unexpected section header '\arguments' Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:42: unknown macro '\item' Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:50: unexpected section header '\arguments' Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:51: unknown macro '\item' Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:59: unexpected section header '\arguments' Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:60: unknown macro '\item' Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:63: unknown macro '\item' Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:66: unknown macro '\item' Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:69: unknown macro '\item' Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:72: unknown macro '\item' Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:80: unexpected section header '\arguments' Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:81: unknown macro '\item' Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:84: unknown macro '\item' Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:87: unknown macro '\item' Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:90: unknown macro '\item' Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:98: unexpected section header '\arguments' Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:99: unknown macro '\item' Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:102: unknown macro '\item' Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:105: unknown macro '\item' Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:108: unknown macro '\item' Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:116: unexpected section header '\arguments' Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:117: unknown macro '\item' Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:120: unknown macro '\item' Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:123: unknown macro '\item' Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:126: unknown macro '\item' Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:134: unexpected section header '\arguments' Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:135: unknown macro '\item' Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:138: unknown macro '\item' Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:141: unknown macro '\item' Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:144: unknown macro '\item' Warning: /home/biocbuild/bbs-3.12-bioc/meat/InterMineR/man/ListManager-methods.Rd:147: unknown macro '\item' *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: multiple methods tables found for ‘union’ Warning: multiple methods tables found for ‘intersect’ ** testing if installed package can be loaded from final location Warning: multiple methods tables found for ‘union’ Warning: multiple methods tables found for ‘intersect’ ** testing if installed package keeps a record of temporary installation path * DONE (InterMineR)
InterMineR.Rcheck/InterMineR-Ex.timings
| name | user | system | elapsed | |
| InterMineR-methods | 0.292 | 0.004 | 0.900 | |
| ListManager-methods | 0 | 0 | 0 | |
| PL_DiabetesGenes | 0.004 | 0.000 | 0.003 | |
| PL_FlyTF_site_specific_TFs | 0.000 | 0.000 | 0.001 | |
| convertToGRanges | 0.632 | 0.012 | 2.886 | |
| convertToGeneAnswers | 0 | 0 | 0 | |
| convertToRangedSummarizedExperiment | 4.576 | 0.032 | 9.057 | |
| doEnrichment | 0 | 0 | 0 | |
| getDatasets | 0.252 | 0.008 | 2.038 | |
| getGeneIds | 0.596 | 0.008 | 3.287 | |
| getModel | 0 | 0 | 0 | |
| getRelease | 0.032 | 0.000 | 0.325 | |
| getTemplateQuery | 0.028 | 0.000 | 0.325 | |
| getTemplates | 0.032 | 0.004 | 0.530 | |
| getVersion | 0.028 | 0.000 | 0.329 | |
| getWidgets | 0.072 | 0.000 | 0.660 | |
| initInterMine | 0 | 0 | 0 | |
| listDatasets | 0 | 0 | 0 | |
| listMines | 0.016 | 0.004 | 0.218 | |
| list_manager | 0 | 0 | 0 | |
| newQuery | 0.000 | 0.000 | 0.001 | |
| runQuery | 4.176 | 0.012 | 7.443 | |
| setConstraints | 0.048 | 0.000 | 0.559 | |
| setQuery | 0.052 | 0.000 | 0.505 | |
| simplifyResult | 11.396 | 0.024 | 14.034 | |
| summary | 0.036 | 0.004 | 0.347 | |