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BioC 3.0: CHECK report for customProDB on moscato1

This page was generated on 2015-04-10 09:49:06 -0700 (Fri, 10 Apr 2015).

Package 216/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
customProDB 1.6.0
xiaojing wang
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/customProDB
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ WARNINGS ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  WARNINGS  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK 

Summary

Package: customProDB
Version: 1.6.0
Command: rm -rf customProDB.buildbin-libdir customProDB.Rcheck && mkdir customProDB.buildbin-libdir customProDB.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=customProDB.buildbin-libdir customProDB_1.6.0.tar.gz >customProDB.Rcheck\00install.out 2>&1 && cp customProDB.Rcheck\00install.out customProDB-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=customProDB.buildbin-libdir --install="check:customProDB-install.out" --force-multiarch --no-vignettes --timings customProDB_1.6.0.tar.gz
StartedAt: 2015-04-10 00:15:08 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 00:28:26 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 797.9 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: customProDB.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf customProDB.buildbin-libdir customProDB.Rcheck && mkdir customProDB.buildbin-libdir customProDB.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=customProDB.buildbin-libdir customProDB_1.6.0.tar.gz >customProDB.Rcheck\00install.out 2>&1 && cp customProDB.Rcheck\00install.out customProDB-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=customProDB.buildbin-libdir --install="check:customProDB-install.out" --force-multiarch --no-vignettes --timings customProDB_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/customProDB.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-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 '1.6.0'
* 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 ... 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
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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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
.parseBMMartParams: no visible global function definition for
  'isSingleString'
Bed2Range: no visible binding for global variable 'V5'
InputVcf: no visible global function definition for 'DataFrame'
InputVcf: no visible binding for global variable 'DataFrame'
InputVcf : <anonymous>: no visible global function definition for
  'DataFrame'
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 global function definition for
  'genome<-'
PrepareAnnotationEnsembl: no visible binding for global variable
  'ensembl_gene_id'
PrepareAnnotationEnsembl: no visible binding for global variable
  'pro_name'
PrepareAnnotationEnsembl: no visible binding for global variable
  'tx_name'
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
  'genome<-'
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'
calculateRPKM: no visible global function definition for
  'keepSeqlevels'
joinDataFrameWithName2Val: no visible global function definition for
  'isSingleString'
setDataFrameColClass: no visible global function definition for
  'isTRUEorFALSE'
* 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' ... [249s] WARNING
Found the following significant warnings:

  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
                          user system elapsed
PrepareAnnotationRefseq  28.66   0.29   86.32
easyRun_mul               5.29   0.03    5.34
PrepareAnnotationEnsembl  3.27   0.28  119.66
** running examples for arch 'x64' ... [161s] WARNING
Found the following significant warnings:

  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
                          user system elapsed
PrepareAnnotationRefseq  30.07   0.48   91.57
easyRun_mul               5.88   0.04    5.96
PrepareAnnotationEnsembl  2.57   0.34   25.32
* 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

WARNING: There were 2 warnings.
NOTE: There were 3 notes.
See
  'D:/biocbld/bbs-3.0-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_1.6.0.zip
* DONE (customProDB)

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

nameusersystemelapsed
Bed2Range0.100.000.09
InputVcf0.640.010.66
JunctionType1.750.031.77
Multiple_VCF1.020.021.04
OutputNovelJun2.780.064.48
OutputVarproseq1.270.001.27
OutputVarproseq_single1.240.011.28
Outputaberrant0.460.020.59
Outputproseq1.180.001.19
OutputsharedPro3.950.033.97
Positionincoding0.920.000.92
PrepareAnnotationEnsembl 3.27 0.28119.66
PrepareAnnotationRefseq28.66 0.2986.32
SharedJunc0.860.000.86
Varlocation000
aaVariation0.900.021.62
calculateRPKM0.990.000.98
easyRun2.150.002.15
easyRun_mul5.290.035.34

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

nameusersystemelapsed
Bed2Range0.140.000.14
InputVcf0.840.010.86
JunctionType2.530.022.54
Multiple_VCF1.240.031.28
OutputNovelJun3.000.013.01
OutputVarproseq1.010.001.02
OutputVarproseq_single0.940.002.31
Outputaberrant0.480.000.48
Outputproseq1.200.021.21
OutputsharedPro3.590.003.59
Positionincoding0.880.000.87
PrepareAnnotationEnsembl 2.57 0.3425.32
PrepareAnnotationRefseq30.07 0.4891.57
SharedJunc0.950.020.97
Varlocation000
aaVariation0.970.000.97
calculateRPKM1.060.011.07
easyRun2.450.042.90
easyRun_mul5.880.045.96