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BioC 3.1: CHECK report for GenomicFeatures on moscato2

This page was generated on 2015-10-09 09:28:38 -0700 (Fri, 09 Oct 2015).

Package 397/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicFeatures 1.20.6
Bioconductor Package Maintainer
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/GenomicFeatures
Last Changed Rev: 108989 / Revision: 109384
Last Changed Date: 2015-09-29 23:24:53 -0700 (Tue, 29 Sep 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  ERROR 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ ERROR ] OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  ERROR  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  ERROR  OK 

Summary

Package: GenomicFeatures
Version: 1.20.6
Command: rm -rf GenomicFeatures.buildbin-libdir GenomicFeatures.Rcheck && mkdir GenomicFeatures.buildbin-libdir GenomicFeatures.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomicFeatures.buildbin-libdir GenomicFeatures_1.20.6.tar.gz >GenomicFeatures.Rcheck\00install.out 2>&1 && cp GenomicFeatures.Rcheck\00install.out GenomicFeatures-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=GenomicFeatures.buildbin-libdir --install="check:GenomicFeatures-install.out" --force-multiarch --no-vignettes --timings GenomicFeatures_1.20.6.tar.gz
StartedAt: 2015-10-09 02:09:02 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 02:29:20 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 1218.1 seconds
RetCode: 1
Status:  ERROR  
CheckDir: GenomicFeatures.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf GenomicFeatures.buildbin-libdir GenomicFeatures.Rcheck && mkdir GenomicFeatures.buildbin-libdir GenomicFeatures.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomicFeatures.buildbin-libdir GenomicFeatures_1.20.6.tar.gz >GenomicFeatures.Rcheck\00install.out 2>&1 && cp GenomicFeatures.Rcheck\00install.out GenomicFeatures-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=GenomicFeatures.buildbin-libdir --install="check:GenomicFeatures-install.out" --force-multiarch --no-vignettes --timings GenomicFeatures_1.20.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/GenomicFeatures.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GenomicFeatures/DESCRIPTION' ... OK
* this is package 'GenomicFeatures' version '1.20.6'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'BiocGenerics' 'S4Vectors' 'IRanges' 'GenomeInfoDb' 'GenomicRanges'
  'AnnotationDbi'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'GenomicFeatures' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
'library' or 'require' calls in package code:
  'FDb.UCSC.tRNAs' 'mirbase.db'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
':::' call which should be '::': 'AnnotationDbi:::dbconn'
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  'AnnotationDbi:::.colsArgumentWarning'
  'AnnotationDbi:::.getMetaValue' 'AnnotationDbi:::.resort'
  'AnnotationDbi:::.testForValidKeytype'
  'AnnotationDbi:::.testSelectArgs' 'AnnotationDbi:::.valid.colnames'
  'AnnotationDbi:::.valid.metadata.table'
  'AnnotationDbi:::.valid.table.colnames' 'AnnotationDbi:::dbEasyQuery'
  'AnnotationDbi:::dbQuery' 'AnnotationDbi:::smartKeys'
  'biomaRt:::martBM' 'biomaRt:::martDataset' 'biomaRt:::martHost'
  'rtracklayer:::resourceDescription' 'rtracklayer:::ucscTableOutputs'
  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
.microRNAs: no visible global function definition for 'mirbase_dbconn'
supportedMiRBaseBuildValues: no visible global function definition for
  'toTable'
supportedMiRBaseBuildValues: no visible binding for global variable
  'mirbaseSPECIES'
* checking Rd files ... NOTE
prepare_Rd: makeTxDbFromGRanges.Rd:38-39: Dropping empty section \details
* 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' ... ERROR
Running examples in 'GenomicFeatures-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: makeTxDbFromBiomart
> ### Title: Make a TxDb object from annotations available on a BioMart
> ###   database
> ### Aliases: makeTxDbFromBiomart getChromInfoFromBiomart
> ###   makeTranscriptDbFromBiomart
> 
> ### ** Examples
> 
> ## ---------------------------------------------------------------------
> ## A. BASIC USAGE
> ## ---------------------------------------------------------------------
> 
> ## We can use listDatasets() from the biomaRt package to list the
> ## datasets available in the "ensembl" BioMart database:
> library(biomaRt)
> head(listDatasets(useMart("ensembl")))
                         dataset                                description
1         oanatinus_gene_ensembl     Ornithorhynchus anatinus genes (OANA5)
2        cporcellus_gene_ensembl            Cavia porcellus genes (cavPor3)
3        gaculeatus_gene_ensembl     Gasterosteus aculeatus genes (BROADS1)
4         lafricana_gene_ensembl         Loxodonta africana genes (loxAfr3)
5 itridecemlineatus_gene_ensembl Ictidomys tridecemlineatus genes (spetri2)
6        choffmanni_gene_ensembl        Choloepus hoffmanni genes (choHof1)
  version
1   OANA5
2 cavPor3
3 BROADS1
4 loxAfr3
5 spetri2
6 choHof1
> 
> ## Retrieve the full transcript dataset for Worm:
> txdb1 <- makeTxDbFromBiomart(dataset="celegans_gene_ensembl")
Download and preprocess the 'transcripts' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... OK
Download and preprocess the 'splicings' data frame ... OK
Download and preprocess the 'genes' data frame ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
> txdb1
TxDb object:
# Db type: TxDb
# Supporting package: GenomicFeatures
# Data source: BioMart
# Organism: Caenorhabditis elegans
# Resource URL: www.biomart.org:80
# BioMart database: ensembl
# BioMart database version: ENSEMBL GENES 81 (SANGER UK)
# BioMart dataset: celegans_gene_ensembl
# BioMart dataset description: Caenorhabditis elegans genes (WBcel235)
# BioMart dataset version: WBcel235
# Full dataset: yes
# miRBase build ID: NA
# transcript_nrow: 57834
# exon_nrow: 173506
# cds_nrow: 131562
# Db created by: GenomicFeatures package from Bioconductor
# Creation time: 2015-10-09 02:19:06 -0700 (Fri, 09 Oct 2015)
# GenomicFeatures version at creation time: 1.20.6
# RSQLite version at creation time: 1.0.0
# DBSCHEMAVERSION: 1.1
> 
> ## Retrieve an incomplete transcript dataset for Human:
> transcript_ids <- c(
+     "ENST00000013894",
+     "ENST00000268655",
+     "ENST00000313243",
+     "ENST00000435657",
+     "ENST00000384428",
+     "ENST00000478783"
+ )
> txdb2 <- makeTxDbFromBiomart(dataset="hsapiens_gene_ensembl",
+                              transcript_ids=transcript_ids)
Download and preprocess the 'transcripts' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... OK
Download and preprocess the 'splicings' data frame ... OK
Download and preprocess the 'genes' data frame ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
> txdb2  # note that these annotations match the GRCh38 genome assembly
TxDb object:
# Db type: TxDb
# Supporting package: GenomicFeatures
# Data source: BioMart
# Organism: Homo sapiens
# Resource URL: www.biomart.org:80
# BioMart database: ensembl
# BioMart database version: ENSEMBL GENES 81 (SANGER UK)
# BioMart dataset: hsapiens_gene_ensembl
# BioMart dataset description: Homo sapiens genes (GRCh38.p3)
# BioMart dataset version: GRCh38.p3
# Full dataset: no
# miRBase build ID: NA
# transcript_nrow: 6
# exon_nrow: 56
# cds_nrow: 48
# Db created by: GenomicFeatures package from Bioconductor
# Creation time: 2015-10-09 02:19:23 -0700 (Fri, 09 Oct 2015)
# GenomicFeatures version at creation time: 1.20.6
# RSQLite version at creation time: 1.0.0
# DBSCHEMAVERSION: 1.1
> 
> ## ---------------------------------------------------------------------
> ## B. USING A HOST OTHER THAN www.biomart.org
> ## ---------------------------------------------------------------------
> 
> ## A typical use case is to access the "ensembl" BioMart database on a
> ## mirror e.g. on uswest.ensembl.org. A gotcha when doing this is that
> ## the name of the database on the mirror can be different! We can check
> ## this with listMarts() from the biomaRt package:
> listMarts(host="uswest.ensembl.org")
               biomart               version
1 ENSEMBL_MART_ENSEMBL      Ensembl Genes 82
2     ENSEMBL_MART_SNP  Ensembl Variation 82
3 ENSEMBL_MART_FUNCGEN Ensembl Regulation 82
4    ENSEMBL_MART_VEGA               Vega 62
5                pride        PRIDE (EBI UK)
> 
> ## Therefore, in addition to setting 'host' to "uswest.ensembl.org" we
> ## must also change the name passed to the 'biomart' argument:
> txdb3 <- makeTxDbFromBiomart(biomart="ENSEMBL_MART_ENSEMBL",
+                              dataset="hsapiens_gene_ensembl",
+                              transcript_ids=transcript_ids,
+                              host="uswest.ensembl.org")
Download and preprocess the 'transcripts' data frame ... Error in getBM(attributes, filters = bm_filters, values = bm_values, ...) : 
  Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_82: DBI connect('database=ensembl_mart_82;host=martdb.local.cloud.local;port=3306','ensro',...) failed: Unknown database 'ensembl_mart_82' at /ensemblweb/www/www_82/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98.
Calls: makeTxDbFromBiomart -> .makeBiomartTranscripts -> .getBM2 -> getBM
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'GenomicFeatures-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: makeTxDbFromBiomart
> ### Title: Make a TxDb object from annotations available on a BioMart
> ###   database
> ### Aliases: makeTxDbFromBiomart getChromInfoFromBiomart
> ###   makeTranscriptDbFromBiomart
> 
> ### ** Examples
> 
> ## ---------------------------------------------------------------------
> ## A. BASIC USAGE
> ## ---------------------------------------------------------------------
> 
> ## We can use listDatasets() from the biomaRt package to list the
> ## datasets available in the "ensembl" BioMart database:
> library(biomaRt)
> head(listDatasets(useMart("ensembl")))
                         dataset                                description
1         oanatinus_gene_ensembl     Ornithorhynchus anatinus genes (OANA5)
2        cporcellus_gene_ensembl            Cavia porcellus genes (cavPor3)
3        gaculeatus_gene_ensembl     Gasterosteus aculeatus genes (BROADS1)
4         lafricana_gene_ensembl         Loxodonta africana genes (loxAfr3)
5 itridecemlineatus_gene_ensembl Ictidomys tridecemlineatus genes (spetri2)
6        choffmanni_gene_ensembl        Choloepus hoffmanni genes (choHof1)
  version
1   OANA5
2 cavPor3
3 BROADS1
4 loxAfr3
5 spetri2
6 choHof1
> 
> ## Retrieve the full transcript dataset for Worm:
> txdb1 <- makeTxDbFromBiomart(dataset="celegans_gene_ensembl")
Download and preprocess the 'transcripts' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... OK
Download and preprocess the 'splicings' data frame ... OK
Download and preprocess the 'genes' data frame ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
> txdb1
TxDb object:
# Db type: TxDb
# Supporting package: GenomicFeatures
# Data source: BioMart
# Organism: Caenorhabditis elegans
# Resource URL: www.biomart.org:80
# BioMart database: ensembl
# BioMart database version: ENSEMBL GENES 81 (SANGER UK)
# BioMart dataset: celegans_gene_ensembl
# BioMart dataset description: Caenorhabditis elegans genes (WBcel235)
# BioMart dataset version: WBcel235
# Full dataset: yes
# miRBase build ID: NA
# transcript_nrow: 57834
# exon_nrow: 173506
# cds_nrow: 131562
# Db created by: GenomicFeatures package from Bioconductor
# Creation time: 2015-10-09 02:24:26 -0700 (Fri, 09 Oct 2015)
# GenomicFeatures version at creation time: 1.20.6
# RSQLite version at creation time: 1.0.0
# DBSCHEMAVERSION: 1.1
> 
> ## Retrieve an incomplete transcript dataset for Human:
> transcript_ids <- c(
+     "ENST00000013894",
+     "ENST00000268655",
+     "ENST00000313243",
+     "ENST00000435657",
+     "ENST00000384428",
+     "ENST00000478783"
+ )
> txdb2 <- makeTxDbFromBiomart(dataset="hsapiens_gene_ensembl",
+                              transcript_ids=transcript_ids)
Download and preprocess the 'transcripts' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... OK
Download and preprocess the 'splicings' data frame ... OK
Download and preprocess the 'genes' data frame ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
> txdb2  # note that these annotations match the GRCh38 genome assembly
TxDb object:
# Db type: TxDb
# Supporting package: GenomicFeatures
# Data source: BioMart
# Organism: Homo sapiens
# Resource URL: www.biomart.org:80
# BioMart database: ensembl
# BioMart database version: ENSEMBL GENES 81 (SANGER UK)
# BioMart dataset: hsapiens_gene_ensembl
# BioMart dataset description: Homo sapiens genes (GRCh38.p3)
# BioMart dataset version: GRCh38.p3
# Full dataset: no
# miRBase build ID: NA
# transcript_nrow: 6
# exon_nrow: 56
# cds_nrow: 48
# Db created by: GenomicFeatures package from Bioconductor
# Creation time: 2015-10-09 02:24:45 -0700 (Fri, 09 Oct 2015)
# GenomicFeatures version at creation time: 1.20.6
# RSQLite version at creation time: 1.0.0
# DBSCHEMAVERSION: 1.1
> 
> ## ---------------------------------------------------------------------
> ## B. USING A HOST OTHER THAN www.biomart.org
> ## ---------------------------------------------------------------------
> 
> ## A typical use case is to access the "ensembl" BioMart database on a
> ## mirror e.g. on uswest.ensembl.org. A gotcha when doing this is that
> ## the name of the database on the mirror can be different! We can check
> ## this with listMarts() from the biomaRt package:
> listMarts(host="uswest.ensembl.org")
               biomart               version
1 ENSEMBL_MART_ENSEMBL      Ensembl Genes 82
2     ENSEMBL_MART_SNP  Ensembl Variation 82
3 ENSEMBL_MART_FUNCGEN Ensembl Regulation 82
4    ENSEMBL_MART_VEGA               Vega 62
5                pride        PRIDE (EBI UK)
> 
> ## Therefore, in addition to setting 'host' to "uswest.ensembl.org" we
> ## must also change the name passed to the 'biomart' argument:
> txdb3 <- makeTxDbFromBiomart(biomart="ENSEMBL_MART_ENSEMBL",
+                              dataset="hsapiens_gene_ensembl",
+                              transcript_ids=transcript_ids,
+                              host="uswest.ensembl.org")
Download and preprocess the 'transcripts' data frame ... Error in getBM(attributes, filters = bm_filters, values = bm_values, ...) : 
  Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_82: DBI connect('database=ensembl_mart_82;host=martdb.local.cloud.local;port=3306','ensro',...) failed: Unknown database 'ensembl_mart_82' at /ensemblweb/www/www_82/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98.
Calls: makeTxDbFromBiomart -> .makeBiomartTranscripts -> .getBM2 -> getBM
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'GenomicFeatures_unit_tests.R' [130s]
 [130s] OK
** running tests for arch 'x64' ...
  Running 'GenomicFeatures_unit_tests.R' [136s]
 [136s] OK
* 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: 2 ERRORs, 4 NOTEs
See
  'E:/biocbld/bbs-3.1-bioc/meat/GenomicFeatures.Rcheck/00check.log'
for details.

GenomicFeatures.Rcheck/00install.out:


install for i386

* installing *source* package 'GenomicFeatures' ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'

install for x64

* installing *source* package 'GenomicFeatures' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'GenomicFeatures' as GenomicFeatures_1.20.6.zip
* DONE (GenomicFeatures)

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

nameusersystemelapsed
DEFAULT_CIRC_SEQS000
FeatureDb-class0.020.010.03
TxDb-class0.790.271.07
as-format-methods0.780.030.81
coordinate-mapping-methods50.88 1.0887.94
extractTranscriptSeqs9.690.069.84
extractUpstreamSeqs 3.17 0.1953.54
features0.060.000.06
getPromoterSeq-methods0.910.010.92
id2name0.030.000.03
makeFeatureDbFromUCSC 8.75 0.4481.35
makeTxDb0.090.000.09

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

nameusersystemelapsed
DEFAULT_CIRC_SEQS000
FeatureDb-class0.030.000.03
TxDb-class0.980.241.37
as-format-methods0.860.030.89
coordinate-mapping-methods45.81 0.9846.82
extractTranscriptSeqs14.99 0.0215.02
extractUpstreamSeqs3.310.093.40
features0.130.000.12
getPromoterSeq-methods1.060.001.06
id2name0.040.000.03
makeFeatureDbFromUCSC11.63 1.1296.38
makeTxDb0.160.000.15