customProDB 1.13.1
xiaojing wang
| Snapshot Date: 2016-07-18 19:15:14 -0700 (Mon, 18 Jul 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/customProDB | | Last Changed Rev: 119227 / Revision: 119445 | | Last Changed Date: 2016-07-08 17:10:59 -0700 (Fri, 08 Jul 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | OK | OK | [ ERROR ] | | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | ERROR | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings customProDB_1.13.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/customProDB.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘customProDB/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘customProDB’ version ‘1.13.1’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘customProDB’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘IRanges’ ‘biomaRt’ ‘AnnotationDbi’
A package should be listed in only one of these fields.
* 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
Unexported objects imported by ':::' calls:
‘biomaRt:::martBM’ ‘biomaRt:::martDataset’ ‘biomaRt:::martHost’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.Ensembl.getTable: no visible global function definition for
‘download.file’
.Ensembl.getTable: no visible global function definition for
‘read.table’
.getDatasetAttrGroups: no visible global function definition for ‘is’
.makeBiomartChrominfo: no visible global function definition for ‘is’
.parseBMMartParams: no visible global function definition for ‘is’
Bed2Range: no visible global function definition for ‘read.table’
Bed2Range: no visible binding for global variable ‘V5’
OutputNovelJun: no visible binding for global variable ‘jun_type’
OutputVarproseq: no visible binding for global variable ‘genename’
OutputVarproseq: no visible binding for global variable ‘txname’
OutputVarproseq: no visible binding for global variable ‘proname’
OutputVarproseq: no visible binding for global variable ‘aaref’
OutputVarproseq: no visible binding for global variable ‘aapos’
OutputVarproseq: no visible binding for global variable ‘aavar’
OutputVarproseq: no visible binding for global variable ‘rsid’
OutputVarproseq_single: no visible binding for global variable
‘genename’
OutputVarproseq_single: no visible binding for global variable ‘txname’
OutputVarproseq_single: no visible binding for global variable
‘proname’
OutputVarproseq_single: no visible binding for global variable ‘aaref’
OutputVarproseq_single: no visible binding for global variable ‘aapos’
OutputVarproseq_single: no visible binding for global variable ‘aavar’
OutputVarproseq_single: no visible binding for global variable ‘rsid’
Outputaberrant: no visible binding for global variable ‘pro_name’
Positionincoding: no visible binding for global variable ‘cds_start’
Positionincoding: no visible binding for global variable ‘cds_end’
PrepareAnnotationEnsembl: no visible binding for global variable
‘ensembl_gene_id’
PrepareAnnotationEnsembl: no visible binding for global variable
‘pro_name’
PrepareAnnotationEnsembl: no visible global function definition for
‘saveDb’
PrepareAnnotationEnsembl: no visible binding for global variable
‘chrom’
PrepareAnnotationEnsembl: no visible binding for global variable ‘name’
PrepareAnnotationEnsembl: no visible binding for global variable
‘alleleCount’
PrepareAnnotationEnsembl: no visible binding for global variable
‘alleles’
PrepareAnnotationRefseq: no visible global function definition for
‘saveDb’
PrepareAnnotationRefseq: no visible binding for global variable
‘mrnaAcc’
PrepareAnnotationRefseq: no visible binding for global variable ‘name’
PrepareAnnotationRefseq: no visible binding for global variable
‘protAcc’
PrepareAnnotationRefseq: no visible binding for global variable
‘transcript’
PrepareAnnotationRefseq: no visible binding for global variable ‘chrom’
PrepareAnnotationRefseq: no visible binding for global variable
‘alleleCount’
PrepareAnnotationRefseq: no visible binding for global variable
‘alleles’
SharedJunc: no visible binding for global variable ‘allsample’
Varlocation: no visible binding for global variable ‘pro_name’
easyRun: no visible global function definition for ‘write.table’
easyRun_mul: no visible global function definition for ‘write.table’
getMartAttribList: no visible global function definition for ‘is’
setDataFrameColClass : <anonymous>: no visible global function
definition for ‘as’
Undefined global functions or variables:
V5 aapos aaref aavar alleleCount alleles allsample as cds_end
cds_start chrom download.file ensembl_gene_id genename is jun_type
mrnaAcc name pro_name proname protAcc read.table rsid saveDb
transcript txname write.table
Consider adding
importFrom("methods", "as", "is")
importFrom("utils", "download.file", "read.table", "write.table")
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 ... WARNING
Undocumented arguments in documentation object 'OutputVarprocodingseq'
‘procodingseq’
Documented arguments not in \usage in documentation object 'OutputVarprocodingseq':
‘proteinseq’
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘customProDB-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PrepareAnnotationEnsembl
> ### Title: prepare annotation from ENSEMBL
> ### Aliases: PrepareAnnotationEnsembl
>
> ### ** Examples
>
> ensembl <- useMart("ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl",
+ host="feb2012.archive.ensembl.org", path="/biomart/martservice",
+ archive=FALSE)
Entity 'nbsp' not defined
Entity 'hellip' not defined
Entity 'hellip' not defined
Entity 'nbsp' not defined
Entity 'raquo' not defined
Entity 'hellip' not defined
Entity 'hellip' not defined
Entity 'hellip' not defined
Entity 'hellip' not defined
Entity 'hellip' not defined
Opening and ending tag mismatch: img line 68 and li
Opening and ending tag mismatch: li line 68 and ul
Opening and ending tag mismatch: ul line 67 and div
Entity 'copy' not defined
Opening and ending tag mismatch: div line 19 and body
Opening and ending tag mismatch: body line 17 and html
Premature end of data in tag html line 2
Error: 1: Entity 'nbsp' not defined
2: Entity 'hellip' not defined
3: Entity 'hellip' not defined
4: Entity 'nbsp' not defined
5: Entity 'raquo' not defined
6: Entity 'hellip' not defined
7: Entity 'hellip' not defined
8: Entity 'hellip' not defined
9: Entity 'hellip' not defined
10: Entity 'hellip' not defined
11: Opening and ending tag mismatch: img line 68 and li
12: Opening and ending tag mismatch: li line 68 and ul
13: Opening and ending tag mismatch: ul line 67 and div
14: Entity 'copy' not defined
15: Opening and ending tag mismatch: div line 19 and body
16: Opening and ending tag mismatch: body line 17 and html
17: Premature end of data in tag html line 2
Execution halted
* 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: 1 ERROR, 1 WARNING, 3 NOTEs
See
‘/home/biocbuild/bbs-3.4-bioc/meat/customProDB.Rcheck/00check.log’
for details.