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BioC 3.4: CHECK report for customProDB on tokay1

This page was generated on 2017-04-15 16:17:57 -0400 (Sat, 15 Apr 2017).

Package 288/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
customProDB 1.14.1
xiaojing wang
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/customProDB
Last Changed Rev: 126611 / Revision: 128728
Last Changed Date: 2017-02-08 17:38:12 -0500 (Wed, 08 Feb 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: customProDB
Version: 1.14.1
Command: rm -rf customProDB.buildbin-libdir customProDB.Rcheck && mkdir customProDB.buildbin-libdir customProDB.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=customProDB.buildbin-libdir customProDB_1.14.1.tar.gz >customProDB.Rcheck\00install.out 2>&1 && cp customProDB.Rcheck\00install.out customProDB-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=customProDB.buildbin-libdir --install="check:customProDB-install.out" --force-multiarch --no-vignettes --timings customProDB_1.14.1.tar.gz
StartedAt: 2017-04-14 21:47:47 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 21:58:29 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 642.1 seconds
RetCode: 0
Status:  OK  
CheckDir: customProDB.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf customProDB.buildbin-libdir customProDB.Rcheck && mkdir customProDB.buildbin-libdir customProDB.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=customProDB.buildbin-libdir customProDB_1.14.1.tar.gz >customProDB.Rcheck\00install.out 2>&1 && cp customProDB.Rcheck\00install.out customProDB-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=customProDB.buildbin-libdir --install="check:customProDB-install.out" --force-multiarch --no-vignettes --timings customProDB_1.14.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/customProDB.Rcheck'
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'customProDB/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'customProDB' version '1.14.1'
* 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 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
* 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 ... OK
** 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 ... 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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
PrepareAnnotationRefseq  22.28   0.95  157.26
PrepareAnnotationEnsembl  4.26   0.52   18.60
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
PrepareAnnotationRefseq  18.47   0.66  148.16
PrepareAnnotationEnsembl  5.03   0.33   18.82
* 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.4-bioc/meat/customProDB.Rcheck/00check.log'
for details.


customProDB.Rcheck/00install.out:


install for i386

* installing *source* package 'customProDB' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'customProDB' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'customProDB' as customProDB_1.14.1.zip
* DONE (customProDB)

customProDB.Rcheck/examples_i386/customProDB-Ex.timings:

nameusersystemelapsed
Bed2Range0.050.000.04
InputVcf0.650.060.72
JunctionType0.520.020.53
Multiple_VCF0.380.030.41
OutputNovelJun1.060.034.20
OutputVarprocodingseq0.690.020.70
OutputVarproseq0.430.010.46
OutputVarproseq_single0.470.020.48
Outputaberrant0.250.010.34
Outputproseq0.720.000.72
OutputsharedPro1.620.021.64
Positionincoding0.270.000.26
PrepareAnnotationEnsembl 4.26 0.5218.60
PrepareAnnotationRefseq 22.28 0.95157.26
SharedJunc0.220.000.22
Varlocation000
aaVariation1.190.031.22
calculateRPKM0.450.020.47
easyRun0.950.000.95
easyRun_mul2.120.012.14

customProDB.Rcheck/examples_x64/customProDB-Ex.timings:

nameusersystemelapsed
Bed2Range0.040.000.05
InputVcf0.330.050.37
JunctionType0.550.030.58
Multiple_VCF0.450.030.48
OutputNovelJun1.190.071.25
OutputVarprocodingseq0.540.010.54
OutputVarproseq0.930.020.96
OutputVarproseq_single0.440.060.50
Outputaberrant0.220.030.25
Outputproseq0.590.000.59
OutputsharedPro1.680.031.70
Positionincoding0.280.030.32
PrepareAnnotationEnsembl 5.03 0.3318.82
PrepareAnnotationRefseq 18.47 0.66148.16
SharedJunc0.420.010.44
Varlocation000
aaVariation0.530.020.54
calculateRPKM0.670.000.68
easyRun1.360.001.36
easyRun_mul3.770.063.82