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 12:31:51 -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: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:InterMineR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings InterMineR_1.12.3.tar.gz |
| StartedAt: 2021-05-06 03:52:16 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 03:57:42 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 325.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: InterMineR.Rcheck |
| Warnings: 7 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:InterMineR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings InterMineR_1.12.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/InterMineR.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'InterMineR' can be installed ... WARNING
Found the following significant warnings:
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:41: unexpected section header '\arguments'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:42: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:50: unexpected section header '\arguments'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:51: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:59: unexpected section header '\arguments'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:60: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:63: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:66: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:69: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:72: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:80: unexpected section header '\arguments'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:81: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:84: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:87: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:90: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:98: unexpected section header '\arguments'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:99: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:102: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:105: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:108: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:116: unexpected section header '\arguments'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:117: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:120: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:123: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:126: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:134: unexpected section header '\arguments'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:135: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:138: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:141: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:144: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:147: unknown macro '\item'
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/convertToGRanges.Rd:5: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/convertToGRanges.Rd:8: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/convertToGRanges.Rd:26: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/convertToGRanges.Rd:29: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/convertToGRanges.Rd:32: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/convertToGRanges.Rd:35: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/convertToGRanges.Rd:38: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/convertToGRanges.Rd:41: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/convertToGRanges.Rd:44: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/convertToGRanges.Rd:47: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/convertToGRanges.Rd:56: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/convertToGRanges.Rd:59: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/convertToGRanges.Rd:66: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/convertToGeneAnswers.Rd:8: file link 'GeneAnswers' in package 'GeneAnswers' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/convertToRangedSummarizedExperiment.Rd:5: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/convertToRangedSummarizedExperiment.Rd:8: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/convertToRangedSummarizedExperiment.Rd:43: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/convertToRangedSummarizedExperiment.Rd:46: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/convertToRangedSummarizedExperiment.Rd:52: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/convertToRangedSummarizedExperiment.Rd:54: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/convertToRangedSummarizedExperiment.Rd:58: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/convertToRangedSummarizedExperiment.Rd:61: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/convertToRangedSummarizedExperiment.Rd:69: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Warning: multiple methods tables found for 'union'
Warning: multiple methods tables found for 'intersect'
See 'C:/Users/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
* 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 ... 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
* 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 ... 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
simplifyResult 11.96 0.34 14.42
runQuery 3.27 0.05 5.23
convertToRangedSummarizedExperiment 2.72 0.00 6.04
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
simplifyResult 12.31 0.05 14.44
runQuery 4.94 0.00 6.83
convertToRangedSummarizedExperiment 4.32 0.10 7.96
* 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, 5 NOTEs
See
'C:/Users/biocbuild/bbs-3.12-bioc/meat/InterMineR.Rcheck/00check.log'
for details.
InterMineR.Rcheck/00install.out
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### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/InterMineR_1.12.3.tar.gz && rm -rf InterMineR.buildbin-libdir && mkdir InterMineR.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=InterMineR.buildbin-libdir InterMineR_1.12.3.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL InterMineR_1.12.3.zip && rm InterMineR_1.12.3.tar.gz InterMineR_1.12.3.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
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0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 4505k 100 4505k 0 0 59.8M 0 --:--:-- --:--:-- --:--:-- 61.1M
install for i386
* 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: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:41: unexpected section header '\arguments'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:42: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:50: unexpected section header '\arguments'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:51: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:59: unexpected section header '\arguments'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:60: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:63: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:66: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:69: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:72: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:80: unexpected section header '\arguments'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:81: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:84: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:87: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:90: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:98: unexpected section header '\arguments'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:99: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:102: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:105: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:108: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:116: unexpected section header '\arguments'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:117: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:120: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:123: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:126: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:134: unexpected section header '\arguments'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:135: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:138: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:141: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:144: unknown macro '\item'
Warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/ListManager-methods.Rd:147: unknown macro '\item'
*** installing help indices
converting help for package 'InterMineR'
finding HTML links ... done
InterMineR-class html
InterMineR-methods html
InterMineR-package html
ListManager-class html
ListManager-methods html
PL_DiabetesGenes html
PL_FlyTF_site_specific_TFs html
convertToGRanges html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/convertToGRanges.Rd:5: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/convertToGRanges.Rd:8: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/convertToGRanges.Rd:26: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/convertToGRanges.Rd:29: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/convertToGRanges.Rd:32: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/convertToGRanges.Rd:35: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/convertToGRanges.Rd:38: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/convertToGRanges.Rd:41: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/convertToGRanges.Rd:44: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/convertToGRanges.Rd:47: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/convertToGRanges.Rd:56: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/convertToGRanges.Rd:59: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/convertToGRanges.Rd:66: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
convertToGeneAnswers html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/convertToGeneAnswers.Rd:8: file link 'GeneAnswers' in package 'GeneAnswers' does not exist and so has been treated as a topic
convertToRangedSummarizedExperiment html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/convertToRangedSummarizedExperiment.Rd:5: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/convertToRangedSummarizedExperiment.Rd:8: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/convertToRangedSummarizedExperiment.Rd:43: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/convertToRangedSummarizedExperiment.Rd:46: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/convertToRangedSummarizedExperiment.Rd:52: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/convertToRangedSummarizedExperiment.Rd:54: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/convertToRangedSummarizedExperiment.Rd:58: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/convertToRangedSummarizedExperiment.Rd:61: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI9Kd5X/R.INSTALL1f9014973d97/InterMineR/man/convertToRangedSummarizedExperiment.Rd:69: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
doEnrichment html
getDatasets html
getGeneIds html
getModel html
getRelease html
getTemplateQuery html
getTemplates html
getVersion html
getWidgets html
initInterMine html
listDatasets html
listMines html
list_manager html
newQuery html
runQuery html
setConstraints html
setQuery html
simplifyResult html
summary html
webservice-class html
** 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
install for x64
* installing *source* package 'InterMineR' ...
** testing if installed package can be loaded
Warning: multiple methods tables found for 'union'
Warning: multiple methods tables found for 'intersect'
* MD5 sums
packaged installation of 'InterMineR' as InterMineR_1.12.3.zip
* DONE (InterMineR)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'InterMineR' successfully unpacked and MD5 sums checked
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InterMineR.Rcheck/examples_i386/InterMineR-Ex.timings
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InterMineR.Rcheck/examples_x64/InterMineR-Ex.timings
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