| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-02-08 01:15:10 -0000 (Wed, 08 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
| 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 InterMineR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/InterMineR.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 975/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| InterMineR 1.21.0 (landing page) InterMine Team
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | WARNINGS | |||||||||
| Package: InterMineR |
| Version: 1.21.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:InterMineR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings InterMineR_1.21.0.tar.gz |
| StartedAt: 2023-02-07 05:21:14 -0000 (Tue, 07 Feb 2023) |
| EndedAt: 2023-02-07 05:29:43 -0000 (Tue, 07 Feb 2023) |
| EllapsedTime: 508.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: InterMineR.Rcheck |
| Warnings: 6 |
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### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:InterMineR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings InterMineR_1.21.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/InterMineR.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘InterMineR/DESCRIPTION’ ... OK
* this is package ‘InterMineR’ version ‘1.21.0’
* 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:
.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: ListManager-methods.Rd:41: unexpected section header '\arguments'
Warning: ListManager-methods.Rd:42: unknown macro '\item'
Warning: ListManager-methods.Rd:50: unexpected section header '\arguments'
Warning: ListManager-methods.Rd:51: unknown macro '\item'
Warning: ListManager-methods.Rd:59: unexpected section header '\arguments'
Warning: ListManager-methods.Rd:60: unknown macro '\item'
Warning: ListManager-methods.Rd:63: unknown macro '\item'
Warning: ListManager-methods.Rd:66: unknown macro '\item'
Warning: ListManager-methods.Rd:69: unknown macro '\item'
Warning: ListManager-methods.Rd:72: unknown macro '\item'
Warning: ListManager-methods.Rd:80: unexpected section header '\arguments'
Warning: ListManager-methods.Rd:81: unknown macro '\item'
Warning: ListManager-methods.Rd:84: unknown macro '\item'
Warning: ListManager-methods.Rd:87: unknown macro '\item'
Warning: ListManager-methods.Rd:90: unknown macro '\item'
Warning: ListManager-methods.Rd:98: unexpected section header '\arguments'
Warning: ListManager-methods.Rd:99: unknown macro '\item'
Warning: ListManager-methods.Rd:102: unknown macro '\item'
Warning: ListManager-methods.Rd:105: unknown macro '\item'
Warning: ListManager-methods.Rd:108: unknown macro '\item'
Warning: ListManager-methods.Rd:116: unexpected section header '\arguments'
Warning: ListManager-methods.Rd:117: unknown macro '\item'
Warning: ListManager-methods.Rd:120: unknown macro '\item'
Warning: ListManager-methods.Rd:123: unknown macro '\item'
Warning: ListManager-methods.Rd:126: unknown macro '\item'
Warning: ListManager-methods.Rd:134: unexpected section header '\arguments'
Warning: ListManager-methods.Rd:135: unknown macro '\item'
Warning: ListManager-methods.Rd:138: unknown macro '\item'
Warning: ListManager-methods.Rd:141: unknown macro '\item'
Warning: ListManager-methods.Rd:144: unknown macro '\item'
Warning: ListManager-methods.Rd:147: unknown macro '\item'
Warning: multiple methods tables found for ‘union’
Warning: multiple methods tables found for ‘subtract’
Warning: multiple methods tables found for ‘intersect’
See ‘/home/biocbuild/bbs-3.17-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 ... 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 ... NOTE
Warning: multiple methods tables found for ‘union’
Warning: multiple methods tables found for ‘subtract’
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
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 reshape
Consider adding
importFrom("stats", "reshape")
importFrom("utils", "URLencode")
to your NAMESPACE file.
* checking Rd files ... WARNING
prepare_Rd: ListManager-methods.Rd:41: unexpected section header '\arguments'
prepare_Rd: ListManager-methods.Rd:42: unknown macro '\item'
prepare_Rd: ListManager-methods.Rd:50: unexpected section header '\arguments'
prepare_Rd: ListManager-methods.Rd:51: unknown macro '\item'
prepare_Rd: ListManager-methods.Rd:59: unexpected section header '\arguments'
prepare_Rd: ListManager-methods.Rd:60: unknown macro '\item'
prepare_Rd: ListManager-methods.Rd:63: unknown macro '\item'
prepare_Rd: ListManager-methods.Rd:66: unknown macro '\item'
prepare_Rd: ListManager-methods.Rd:69: unknown macro '\item'
prepare_Rd: ListManager-methods.Rd:72: unknown macro '\item'
prepare_Rd: ListManager-methods.Rd:80: unexpected section header '\arguments'
prepare_Rd: ListManager-methods.Rd:81: unknown macro '\item'
prepare_Rd: ListManager-methods.Rd:84: unknown macro '\item'
prepare_Rd: ListManager-methods.Rd:87: unknown macro '\item'
prepare_Rd: ListManager-methods.Rd:90: unknown macro '\item'
prepare_Rd: ListManager-methods.Rd:98: unexpected section header '\arguments'
prepare_Rd: ListManager-methods.Rd:99: unknown macro '\item'
prepare_Rd: ListManager-methods.Rd:102: unknown macro '\item'
prepare_Rd: ListManager-methods.Rd:105: unknown macro '\item'
prepare_Rd: ListManager-methods.Rd:108: unknown macro '\item'
prepare_Rd: ListManager-methods.Rd:116: unexpected section header '\arguments'
prepare_Rd: ListManager-methods.Rd:117: unknown macro '\item'
prepare_Rd: ListManager-methods.Rd:120: unknown macro '\item'
prepare_Rd: ListManager-methods.Rd:123: unknown macro '\item'
prepare_Rd: ListManager-methods.Rd:126: unknown macro '\item'
prepare_Rd: ListManager-methods.Rd:134: unexpected section header '\arguments'
prepare_Rd: ListManager-methods.Rd:135: unknown macro '\item'
prepare_Rd: ListManager-methods.Rd:138: unknown macro '\item'
prepare_Rd: ListManager-methods.Rd:141: unknown macro '\item'
prepare_Rd: ListManager-methods.Rd:144: unknown macro '\item'
prepare_Rd: 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 ... NOTE
Unknown package ‘GeneAnswers’ in Rd xrefs
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘GET_api_list’ ‘do_operation’ ‘get_unused_list_name’
Undocumented S4 classes:
‘Service’
Undocumented S4 methods:
generic 'GET_api_list' and siglist 'ListManager'
generic 'doEnrichment' and siglist 'Service'
generic 'do_operation' and siglist 'ListManager'
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
Functions or methods with usage in documentation object 'convertToGeneAnswers' but not in code:
‘convertToGeneAnswers’
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 LazyData ... 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 10.194 0.044 17.446
runQuery 2.934 0.008 12.093
convertToRangedSummarizedExperiment 2.749 0.122 10.673
convertToGRanges 1.387 0.004 6.621
getGeneIds 0.427 0.020 10.939
getDatasets 0.162 0.000 5.237
setConstraints 0.028 0.008 36.352
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘InterMineR.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 6 WARNINGs, 5 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/InterMineR.Rcheck/00check.log’
for details.
InterMineR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL InterMineR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-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’ Creating a new generic function for ‘subtract’ in package ‘InterMineR’ ** help Warning: ListManager-methods.Rd:41: unexpected section header '\arguments' Warning: ListManager-methods.Rd:42: unknown macro '\item' Warning: ListManager-methods.Rd:50: unexpected section header '\arguments' Warning: ListManager-methods.Rd:51: unknown macro '\item' Warning: ListManager-methods.Rd:59: unexpected section header '\arguments' Warning: ListManager-methods.Rd:60: unknown macro '\item' Warning: ListManager-methods.Rd:63: unknown macro '\item' Warning: ListManager-methods.Rd:66: unknown macro '\item' Warning: ListManager-methods.Rd:69: unknown macro '\item' Warning: ListManager-methods.Rd:72: unknown macro '\item' Warning: ListManager-methods.Rd:80: unexpected section header '\arguments' Warning: ListManager-methods.Rd:81: unknown macro '\item' Warning: ListManager-methods.Rd:84: unknown macro '\item' Warning: ListManager-methods.Rd:87: unknown macro '\item' Warning: ListManager-methods.Rd:90: unknown macro '\item' Warning: ListManager-methods.Rd:98: unexpected section header '\arguments' Warning: ListManager-methods.Rd:99: unknown macro '\item' Warning: ListManager-methods.Rd:102: unknown macro '\item' Warning: ListManager-methods.Rd:105: unknown macro '\item' Warning: ListManager-methods.Rd:108: unknown macro '\item' Warning: ListManager-methods.Rd:116: unexpected section header '\arguments' Warning: ListManager-methods.Rd:117: unknown macro '\item' Warning: ListManager-methods.Rd:120: unknown macro '\item' Warning: ListManager-methods.Rd:123: unknown macro '\item' Warning: ListManager-methods.Rd:126: unknown macro '\item' Warning: ListManager-methods.Rd:134: unexpected section header '\arguments' Warning: ListManager-methods.Rd:135: unknown macro '\item' Warning: ListManager-methods.Rd:138: unknown macro '\item' Warning: ListManager-methods.Rd:141: unknown macro '\item' Warning: ListManager-methods.Rd:144: unknown macro '\item' Warning: 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 ‘subtract’ 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 ‘subtract’ 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 | 0.146 | 0.000 | 4.320 | |
| ListManager-methods | 0.001 | 0.000 | 0.001 | |
| PL_DiabetesGenes | 0.002 | 0.000 | 0.002 | |
| PL_FlyTF_site_specific_TFs | 0.001 | 0.000 | 0.001 | |
| convertToGRanges | 1.387 | 0.004 | 6.621 | |
| convertToGeneAnswers | 0 | 0 | 0 | |
| convertToRangedSummarizedExperiment | 2.749 | 0.122 | 10.673 | |
| doEnrichment | 0 | 0 | 0 | |
| getDatasets | 0.162 | 0.000 | 5.237 | |
| getGeneIds | 0.427 | 0.020 | 10.939 | |
| getModel | 0.000 | 0.000 | 0.001 | |
| getRelease | 0.022 | 0.000 | 4.713 | |
| getTemplateQuery | 0.022 | 0.000 | 1.636 | |
| getTemplates | 0.026 | 0.008 | 1.754 | |
| getVersion | 0.022 | 0.000 | 1.113 | |
| getWidgets | 0.053 | 0.000 | 2.746 | |
| initInterMine | 0.000 | 0.000 | 0.001 | |
| listDatasets | 0 | 0 | 0 | |
| listMines | 0.012 | 0.000 | 2.401 | |
| list_manager | 0 | 0 | 0 | |
| newQuery | 0.000 | 0.000 | 0.001 | |
| runQuery | 2.934 | 0.008 | 12.093 | |
| setConstraints | 0.028 | 0.008 | 36.352 | |
| setQuery | 0.037 | 0.000 | 3.059 | |
| simplifyResult | 10.194 | 0.044 | 17.446 | |
| summary | 0.031 | 0.000 | 2.335 | |