BioC 3.3: CHECK report for customProDB on moscato2

Package: customProDB

Version: 1.12.1

Command: rm -rf customProDB.buildbin-libdir customProDB.Rcheck && mkdir customProDB.buildbin-libdir customProDB.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=customProDB.buildbin-libdir customProDB_1.12.1.tar.gz >customProDB.Rcheck\00install.out 2>&1 && cp customProDB.Rcheck\00install.out customProDB-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=customProDB.buildbin-libdir --install="check:customProDB-install.out" --force-multiarch --no-vignettes --timings customProDB_1.12.1.tar.gz

StartedAt: 2016-10-13 02:43:09 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 03:01:16 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 1087.1 seconds

RetCode: 0

Status:  OK

CheckDir: customProDB.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf customProDB.buildbin-libdir customProDB.Rcheck && mkdir customProDB.buildbin-libdir customProDB.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=customProDB.buildbin-libdir customProDB_1.12.1.tar.gz >customProDB.Rcheck\00install.out 2>&1 && cp customProDB.Rcheck\00install.out customProDB-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=customProDB.buildbin-libdir --install="check:customProDB-install.out" --force-multiarch --no-vignettes --timings customProDB_1.12.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/customProDB.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '1.12.1'
* 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'
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'
Undefined global functions or variables:
  V5 aapos aaref aavar alleleCount alleles allsample cds_end cds_start
  chrom download.file ensembl_gene_id genename jun_type mrnaAcc name
  pro_name proname protAcc read.table rsid saveDb transcript txname
  write.table
Consider adding
  importFrom("utils", "download.file", "read.table", "write.table")
to your NAMESPACE file.
* 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  28.26   0.46  163.30
PrepareAnnotationEnsembl  5.87   0.57   30.59
easyRun_mul               4.78   0.03   16.13
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
PrepareAnnotationRefseq  34.38   0.75  166.25
PrepareAnnotationEnsembl  6.79   0.82  280.46
easyRun_mul               4.74   0.03    5.10
OutputNovelJun            1.93   0.03   14.48
* 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
  'E:/biocbld/bbs-3.3-bioc/meat/customProDB.Rcheck/00check.log'
for details.

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_1.12.1.zip
* DONE (customProDB)

name	user	system	elapsed
Bed2Range	0.33	0.01	0.34
InputVcf	0.40	0.00	0.41
JunctionType	0.53	0.00	0.53
Multiple_VCF	0.66	0.04	0.69
OutputNovelJun	1.81	0.01	1.88
OutputVarproseq	0.76	0.00	0.77
OutputVarproseq_single	0.50	0.02	1.17
Outputaberrant	0.36	0.03	0.39
Outputproseq	0.73	0.01	0.75
OutputsharedPro	2.30	0.02	2.31
Positionincoding	0.48	0.01	0.50
PrepareAnnotationEnsembl	5.87	0.57	30.59
PrepareAnnotationRefseq	28.26	0.46	163.30
SharedJunc	0.57	0.00	1.42
Varlocation	0	0	0
aaVariation	1.07	0.02	1.46
calculateRPKM	1.34	0.02	2.02
easyRun	2.45	0.03	3.32
easyRun_mul	4.78	0.03	16.13

name	user	system	elapsed
Bed2Range	0.17	0.00	0.64
InputVcf	1.00	0.04	2.32
JunctionType	0.89	0.02	2.51
Multiple_VCF	0.78	0.03	1.10
OutputNovelJun	1.93	0.03	14.48
OutputVarproseq	0.89	0.00	1.63
OutputVarproseq_single	0.87	0.05	0.99
Outputaberrant	0.43	0.01	1.06
Outputproseq	0.96	0.00	2.35
OutputsharedPro	2.75	0.00	3.84
Positionincoding	0.48	0.02	1.37
PrepareAnnotationEnsembl	6.79	0.82	280.46
PrepareAnnotationRefseq	34.38	0.75	166.25
SharedJunc	0.48	0.00	1.38
Varlocation	0	0	0
aaVariation	0.88	0.00	0.87
calculateRPKM	0.82	0.02	0.84
easyRun	2.25	0.03	2.28
easyRun_mul	4.74	0.03	5.10