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Package 30/83HostnameOS / ArchBUILDCHECKBUILD BIN
geneLenDataBase 0.99.4
Matthew Young
Snapshot Date: 2010-09-24 00:28:34 -0700 (Fri, 24 Sep 2010)
URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/geneLenDataBase
Last Changed Rev: 1214 / Revision: 1309
Last Changed Date: 2010-04-21 22:38:13 -0700 (Wed, 21 Apr 2010)
wilson1 Linux (openSUSE 11.1) / x86_64  OK [ OK ]
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  TIMEOUT  OK 

Summary

Package: geneLenDataBase
Version: 0.99.4
Command: /home/biocbuild/bbs-2.6-bioc/R/bin/R CMD check --no-vignettes --timings geneLenDataBase_0.99.4.tar.gz
StartedAt: 2010-09-24 02:26:59 -0700 (Fri, 24 Sep 2010)
EndedAt: 2010-09-24 02:45:49 -0700 (Fri, 24 Sep 2010)
EllapsedTime: 1130.1 seconds
RetCode: 0
Status:  OK 
CheckDir: geneLenDataBase.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.6-data-experiment/meat/geneLenDataBase.Rcheck'
* using R version 2.11.1 (2010-05-31)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'geneLenDataBase/DESCRIPTION' ... OK
* this is package 'geneLenDataBase' version '0.99.4'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'geneLenDataBase' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 data for non-ASCII characters ... OK
* checking examples ... OK
* checking PDF version of manual ... OK

geneLenDataBase.Rcheck/00install.out:

* install options are ' --no-html'

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

* DONE (geneLenDataBase)

geneLenDataBase.Rcheck/geneLenDataBase-Ex.timings:

nameusersystemelapsed
anoCar1.ensGene.LENGTH0.1160.0040.118
anoCar1.genscan.LENGTH0.0720.0320.103
anoCar1.xenoRefGene.LENGTH1.9680.0281.995
anoGam1.ensGene.LENGTH0.4120.0320.444
anoGam1.geneid.LENGTH0.0600.0280.087
anoGam1.genscan.LENGTH0.0520.0400.351
apiMel1.genscan.LENGTH0.0680.0120.078
apiMel2.ensGene.LENGTH0.1040.0200.125
apiMel2.geneid.LENGTH0.0400.0560.094
apiMel2.genscan.LENGTH0.0520.0200.074
aplCal1.xenoRefGene.LENGTH0.5440.0280.570
bosTau2.geneSymbol.LENGTH0.0520.0240.077
bosTau2.geneid.LENGTH0.4160.0160.435
bosTau2.genscan.LENGTH0.5560.0360.594
bosTau2.refGene.LENGTH0.0600.0120.072
bosTau2.sgpGene.LENGTH0.1240.0120.135
bosTau3.ensGene.LENGTH0.1360.0160.152
bosTau3.geneSymbol.LENGTH0.0440.0200.065
bosTau3.geneid.LENGTH0.1960.0240.219
bosTau3.genscan.LENGTH0.1000.0160.117
bosTau3.refGene.LENGTH0.0320.0320.067
bosTau3.sgpGene.LENGTH0.1480.0400.187
bosTau4.ensGene.LENGTH0.2160.0280.244
bosTau4.geneSymbol.LENGTH0.0400.0200.063
bosTau4.genscan.LENGTH0.1000.0120.112
bosTau4.nscanGene.LENGTH0.0400.0240.063
bosTau4.refGene.LENGTH0.0520.0080.062
braFlo1.xenoRefGene.LENGTH0.7360.0320.768
caeJap1.xenoRefGene.LENGTH0.4120.0000.428
caePb1.xenoRefGene.LENGTH0.6000.0080.608
caePb2.xenoRefGene.LENGTH0.5920.0400.629
caeRem2.xenoRefGene.LENGTH0.4640.0040.470
caeRem3.xenoRefGene.LENGTH0.4640.0240.489
calJac1.genscan.LENGTH0.1960.0400.236
calJac1.nscanGene.LENGTH0.1400.0000.138
calJac1.xenoRefGene.LENGTH1.1810.0121.190
canFam1.ensGene.LENGTH0.1280.0120.139
canFam1.geneSymbol.LENGTH0.0920.0000.091
canFam1.genscan.LENGTH0.0920.0040.099
canFam1.nscanGene.LENGTH0.1640.0080.175
canFam1.refGene.LENGTH0.0160.0000.016
canFam1.xenoRefGene.LENGTH0.7240.0280.788
canFam2.ensGene.LENGTH0.1880.0160.207
canFam2.geneSymbol.LENGTH0.0160.0000.016
canFam2.genscan.LENGTH0.0720.0200.095
canFam2.nscanGene.LENGTH0.0800.0120.095
canFam2.refGene.LENGTH0.0120.0040.015
canFam2.xenoRefGene.LENGTH0.8760.0240.903
cavPor3.ensGene.LENGTH0.4320.0080.455
cavPor3.genscan.LENGTH0.1120.0240.135
cavPor3.nscanGene.LENGTH0.0760.0160.091
cavPor3.xenoRefGene.LENGTH0.7560.0520.806
cb1.xenoRefGene.LENGTH0.6840.0040.687
cb3.xenoRefGene.LENGTH0.3960.0200.416
ce2.geneSymbol.LENGTH0.0960.0360.132
ce2.geneid.LENGTH0.5200.0040.528
ce2.refGene.LENGTH0.0840.0360.121
ce4.geneSymbol.LENGTH0.0880.0360.121
ce4.refGene.LENGTH0.0680.0520.160
ce4.xenoRefGene.LENGTH0.0840.0040.090
ce6.ensGene.LENGTH0.100.020.12
ce6.geneSymbol.LENGTH0.0880.0320.121
ce6.refGene.LENGTH0.0800.0400.121
ce6.xenoRefGene.LENGTH0.1080.0080.114
ci1.geneSymbol.LENGTH0.0120.0040.015
ci1.refGene.LENGTH0.0080.0040.014
ci1.xenoRefGene.LENGTH0.2040.0040.210
ci2.ensGene.LENGTH0.0680.0120.080
ci2.geneSymbol.LENGTH0.0160.0000.015
ci2.refGene.LENGTH0.0160.0000.014
ci2.xenoRefGene.LENGTH0.3920.0080.402
danRer3.ensGene.LENGTH0.2200.0320.255
danRer3.geneSymbol.LENGTH0.0720.0240.096
danRer3.refGene.LENGTH0.0560.0320.089
danRer4.ensGene.LENGTH0.1480.0040.151
danRer4.geneSymbol.LENGTH0.0640.0320.093
danRer4.genscan.LENGTH0.1120.0240.138
danRer4.nscanGene.LENGTH0.1960.0160.214
danRer4.refGene.LENGTH0.3840.0280.409
danRer5.ensGene.LENGTH0.1320.0080.139
danRer5.geneSymbol.LENGTH0.0640.0200.085
danRer5.refGene.LENGTH0.0640.0160.080
danRer5.vegaGene.LENGTH0.0640.0160.082
danRer5.vegaPseudoGene.LENGTH0.0120.0000.011
danRer6.ensGene.LENGTH0.1480.0120.160
danRer6.geneSymbol.LENGTH0.0640.0200.084
danRer6.refGene.LENGTH0.0760.0040.082
danRer6.xenoRefGene.LENGTH0.8040.0240.826
dm1.geneSymbol.LENGTH0.4040.0360.441
dm1.genscan.LENGTH0.0360.0200.057
dm1.refGene.LENGTH0.0680.0560.157
dm2.geneSymbol.LENGTH0.0840.0320.114
dm2.geneid.LENGTH0.0520.0200.072
dm2.genscan.LENGTH0.0320.0240.057
dm2.nscanGene.LENGTH0.0560.0040.062
dm2.refGene.LENGTH0.0720.0400.110
dm3.geneSymbol.LENGTH0.0760.0080.083
dm3.nscanPasaGene.LENGTH0.0680.0240.094
dm3.refGene.LENGTH0.0760.0000.077
downloadLengthFromUCSC52.799 0.75277.300
dp2.genscan.LENGTH0.0450.0240.069
dp2.xenoRefGene.LENGTH0.2880.0280.320
dp3.geneid.LENGTH0.0640.0240.088
dp3.genscan.LENGTH0.0480.0160.064
dp3.xenoRefGene.LENGTH0.1400.0320.171
droAna1.geneid.LENGTH0.0920.0160.106
droAna1.genscan.LENGTH0.0320.0240.054
droAna1.xenoRefGene.LENGTH0.2560.0320.288
droAna2.genscan.LENGTH0.0720.0040.076
droAna2.xenoRefGene.LENGTH0.3440.0520.397
droEre1.genscan.LENGTH0.0440.0240.069
droEre1.xenoRefGene.LENGTH0.3440.0320.375
droGri1.genscan.LENGTH0.0560.0320.089
droGri1.xenoRefGene.LENGTH0.3480.0120.363
droMoj1.geneid.LENGTH0.4320.0240.457
droMoj1.genscan.LENGTH0.0720.0040.076
droMoj1.xenoRefGene.LENGTH0.2880.0440.330
droMoj2.genscan.LENGTH0.0520.0280.081
droMoj2.xenoRefGene.LENGTH0.3720.0520.420
droPer1.genscan.LENGTH0.0720.0200.094
droPer1.xenoRefGene.LENGTH0.4640.0440.509
droSec1.genscan.LENGTH0.0520.0200.072
droSec1.xenoRefGene.LENGTH0.5920.0080.598
droSim1.geneid.LENGTH0.0760.0120.087
droSim1.genscan.LENGTH0.0440.0200.063
droSim1.xenoRefGene.LENGTH0.3320.0240.358
droVir1.geneid.LENGTH0.1480.0160.166
droVir1.genscan.LENGTH0.0840.0240.106
droVir1.xenoRefGene.LENGTH0.3640.0360.451
droVir2.genscan.LENGTH0.0600.0200.084
droVir2.xenoRefGene.LENGTH0.4520.0240.564
droYak1.geneid.LENGTH0.0680.0320.102
droYak1.genscan.LENGTH0.0560.0200.079
droYak1.xenoRefGene.LENGTH0.3200.0040.368
droYak2.genscan.LENGTH0.0520.0200.079
droYak2.xenoRefGene.LENGTH0.4480.0560.548
equCab1.geneSymbol.LENGTH0.0120.0000.019
equCab1.geneid.LENGTH0.140.020.17
equCab1.nscanGene.LENGTH0.0600.0320.137
equCab1.refGene.LENGTH0.0160.0000.016
equCab1.sgpGene.LENGTH0.0880.0120.112
equCab2.ensGene.LENGTH0.1800.0280.244
equCab2.geneSymbol.LENGTH0.0160.0000.021
equCab2.nscanGene.LENGTH0.0880.0360.135
equCab2.refGene.LENGTH0.0160.0040.020
equCab2.xenoRefGene.LENGTH0.8080.0240.910
felCat3.ensGene.LENGTH0.1640.0000.215
felCat3.geneSymbol.LENGTH0.0120.0040.014
felCat3.geneid.LENGTH0.9480.0561.070
felCat3.genscan.LENGTH0.1720.0200.205
felCat3.nscanGene.LENGTH0.1400.0160.164
felCat3.refGene.LENGTH0.0160.0000.014
felCat3.sgpGene.LENGTH0.1640.0320.236
felCat3.xenoRefGene.LENGTH1.5720.0441.705
fr1.ensGene.LENGTH0.6080.0400.668
fr1.genscan.LENGTH0.080.020.10
fr2.ensGene.LENGTH0.2200.0400.285
galGal2.ensGene.LENGTH0.0760.0080.088
galGal2.geneSymbol.LENGTH0.0280.0080.036
galGal2.geneid.LENGTH0.0520.0360.095
galGal2.genscan.LENGTH0.0800.0440.187
galGal2.refGene.LENGTH0.0320.0040.035
galGal2.sgpGene.LENGTH0.0760.0240.100
galGal3.ensGene.LENGTH0.1080.0040.110
galGal3.geneSymbol.LENGTH0.0280.0040.034
galGal3.genscan.LENGTH0.0680.0440.112
galGal3.nscanGene.LENGTH0.0920.0000.093
galGal3.refGene.LENGTH0.0240.0120.033
galGal3.xenoRefGene.LENGTH0.6240.0200.644
gasAcu1.ensGene.LENGTH0.1200.0280.149
gasAcu1.nscanGene.LENGTH0.1360.0360.169
hg16.acembly.LENGTH0.5160.0280.546
hg16.ensGene.LENGTH0.1040.0080.112
hg16.exoniphy.LENGTH0.7000.0320.734
hg16.geneSymbol.LENGTH0.1280.0120.143
hg16.geneid.LENGTH0.0640.0480.115
hg16.genscan.LENGTH0.0920.0120.106
hg16.knownGene.LENGTH0.5850.0480.630
hg16.refGene.LENGTH0.1240.0120.136
hg16.sgpGene.LENGTH0.0960.0040.100
hg17.acembly.LENGTH1.1880.0201.209
hg17.acescan.LENGTH0.0120.0120.026
hg17.ccdsGene.LENGTH0.0440.0120.058
hg17.ensGene.LENGTH0.1480.0160.167
hg17.exoniphy.LENGTH0.5040.0200.546
hg17.geneSymbol.LENGTH0.1160.0160.132
hg17.geneid.LENGTH1.0640.0161.083
hg17.genscan.LENGTH0.0760.0160.091
hg17.knownGene.LENGTH0.1200.0200.138
hg17.refGene.LENGTH0.0960.0200.114
hg17.sgpGene.LENGTH0.0800.0240.105
hg17.vegaGene.LENGTH0.0480.0240.069
hg17.vegaPseudoGene.LENGTH0.0280.0040.033
hg17.xenoRefGene.LENGTH0.2280.0200.247
hg18.acembly.LENGTH0.4960.0240.520
hg18.acescan.LENGTH0.0280.0000.025
hg18.ccdsGene.LENGTH0.0520.0200.073
hg18.ensGene.LENGTH0.2200.0200.239
hg18.exoniphy.LENGTH0.4560.0480.507
hg18.geneSymbol.LENGTH0.1120.0160.126
hg18.geneid.LENGTH0.0840.0240.109
hg18.genscan.LENGTH0.0840.0120.093
hg18.knownGene.LENGTH0.1840.0120.195
hg18.knownGeneOld3.LENGTH0.0960.0280.125
hg18.refGene.LENGTH0.1040.0240.125
hg18.sgpGene.LENGTH0.1040.0160.119
hg18.sibGene.LENGTH0.3920.0280.421
hg18.xenoRefGene.LENGTH0.4640.0400.501
hg19.ccdsGene.LENGTH0.0640.0280.092
hg19.ensGene.LENGTH0.3800.0360.414
hg19.exoniphy.LENGTH0.4440.0520.497
hg19.geneSymbol.LENGTH0.1160.0120.128
hg19.knownGene.LENGTH0.2000.0360.238
hg19.nscanGene.LENGTH0.5880.0080.594
hg19.refGene.LENGTH0.1200.0160.134
hg19.xenoRefGene.LENGTH0.4200.0040.424
loxAfr3.xenoRefGene.LENGTH0.9800.0160.994
mm7.ensGene.LENGTH0.1480.0040.291
mm7.geneSymbol.LENGTH0.1240.0040.129
mm7.geneid.LENGTH0.1240.0160.140
mm7.genscan.LENGTH0.1000.0160.116
mm7.knownGene.LENGTH0.1520.0080.161
mm7.refGene.LENGTH0.1080.0080.113
mm7.sgpGene.LENGTH0.1160.0160.134
mm7.xenoRefGene.LENGTH0.4120.0280.442
mm8.ccdsGene.LENGTH0.0400.0160.053
mm8.ensGene.LENGTH0.0960.0160.114
mm8.geneSymbol.LENGTH0.0960.0040.102
mm8.geneid.LENGTH0.1080.0160.122
mm8.genscan.LENGTH0.0840.0080.091
mm8.knownGene.LENGTH0.1280.0080.156
mm8.nscanGene.LENGTH0.0840.0000.083
mm8.refGene.LENGTH0.0920.0040.097
mm8.sgpGene.LENGTH0.1000.0240.121
mm8.sibGene.LENGTH0.6400.0160.670
mm8.xenoRefGene.LENGTH0.4600.0240.486
mm9.acembly.LENGTH0.4480.0120.461
mm9.ccdsGene.LENGTH0.0600.0080.069
mm9.ensGene.LENGTH0.1840.0320.216
mm9.exoniphy.LENGTH1.2680.0361.467
mm9.geneSymbol.LENGTH0.1080.0040.110
mm9.geneid.LENGTH0.1080.0280.162
mm9.genscan.LENGTH0.0890.0160.108
mm9.knownGene.LENGTH0.1480.0320.187
mm9.nscanGene.LENGTH0.0760.0080.084
mm9.refGene.LENGTH0.1000.0040.103
mm9.sgpGene.LENGTH0.1160.0120.128
mm9.xenoRefGene.LENGTH0.4640.0360.518
monDom1.genscan.LENGTH0.0880.0200.107
monDom4.ensGene.LENGTH0.1040.0080.114
monDom4.geneSymbol.LENGTH0.0120.0040.013
monDom4.genscan.LENGTH0.0960.0280.123
monDom4.nscanGene.LENGTH1.0120.0161.030
monDom4.refGene.LENGTH0.0120.0000.012
monDom4.xenoRefGene.LENGTH0.4040.0160.422
monDom5.ensGene.LENGTH0.1160.0040.120
monDom5.geneSymbol.LENGTH0.0120.0000.013
monDom5.genscan.LENGTH0.0600.0080.068
monDom5.nscanGene.LENGTH0.1240.0080.130
monDom5.refGene.LENGTH0.0120.0000.012
monDom5.xenoRefGene.LENGTH0.6440.0280.672
ornAna1.ensGene.LENGTH0.1120.0200.187
ornAna1.geneSymbol.LENGTH0.0080.0000.011
ornAna1.refGene.LENGTH0.0080.0000.010
ornAna1.xenoRefGene.LENGTH0.6080.0320.638
oryLat2.ensGene.LENGTH0.0960.0120.106
oryLat2.geneSymbol.LENGTH0.0120.0000.013
oryLat2.refGene.LENGTH0.0160.0000.013
oryLat2.xenoRefGene.LENGTH0.5640.0240.592
panTro1.ensGene.LENGTH0.1160.0200.135
panTro1.geneid.LENGTH0.0680.0440.110
panTro1.genscan.LENGTH0.0720.0160.087
panTro1.xenoRefGene.LENGTH0.1360.0200.155
panTro2.ensGene.LENGTH0.1200.0200.142
panTro2.geneSymbol.LENGTH0.1160.0160.132
panTro2.genscan.LENGTH0.0680.0200.089
panTro2.nscanGene.LENGTH0.0720.0080.081
panTro2.refGene.LENGTH0.1160.0120.131
panTro2.xenoRefGene.LENGTH0.5720.0120.588
petMar1.xenoRefGene.LENGTH0.3000.0440.346
ponAbe2.ensGene.LENGTH0.1120.0120.156
ponAbe2.geneSymbol.LENGTH0.0280.0000.028
ponAbe2.genscan.LENGTH0.0800.0080.089
ponAbe2.nscanGene.LENGTH0.0720.0040.077
ponAbe2.refGene.LENGTH0.0160.0080.027
ponAbe2.xenoRefGene.LENGTH0.7320.0120.741
priPac1.xenoRefGene.LENGTH0.4440.0160.589
rheMac2.ensGene.LENGTH0.1640.0120.178
rheMac2.geneSymbol.LENGTH0.0120.0040.016
rheMac2.geneid.LENGTH0.0840.0200.104
rheMac2.nscanGene.LENGTH0.0720.0080.084
rheMac2.refGene.LENGTH0.0120.0000.015
rheMac2.sgpGene.LENGTH0.0880.0120.102
rheMac2.xenoRefGene.LENGTH0.6440.0080.650
rn3.ensGene.LENGTH0.1240.0240.149
rn3.geneSymbol.LENGTH0.0760.0200.096
rn3.geneid.LENGTH0.0720.0040.076
rn3.genscan.LENGTH0.0800.0200.098
rn3.knownGene.LENGTH0.0400.0080.049
rn3.nscanGene.LENGTH0.0720.0040.074
rn3.refGene.LENGTH0.0560.0360.094
rn3.sgpGene.LENGTH0.0800.0120.092
rn3.xenoRefGene.LENGTH0.7480.0440.792
rn4.ensGene.LENGTH0.5920.0080.600
rn4.geneSymbol.LENGTH0.1000.0160.114
rn4.geneid.LENGTH0.1240.0320.153
rn4.genscan.LENGTH0.1000.0120.112
rn4.knownGene.LENGTH0.0440.0120.055
rn4.nscanGene.LENGTH0.1040.0200.124
rn4.refGene.LENGTH0.0920.0200.109
rn4.sgpGene.LENGTH0.1040.0320.137
rn4.xenoRefGene.LENGTH0.6160.0400.655
sacCer1.ensGene.LENGTH0.0320.0160.048
sacCer2.ensGene.LENGTH0.0400.0120.101
strPur1.geneSymbol.LENGTH0.0120.0040.015
strPur1.genscan.LENGTH0.1440.0240.166
strPur1.refGene.LENGTH0.0040.0120.016
strPur1.xenoRefGene.LENGTH0.8640.0240.894
strPur2.geneSymbol.LENGTH0.0160.0000.014
strPur2.genscan.LENGTH0.1680.0160.183
strPur2.refGene.LENGTH0.0120.0040.014
strPur2.xenoRefGene.LENGTH1.0520.0241.076
supportedGeneIDs0.0120.0000.012
supportedGenomes0.0400.0000.159
taeGut1.ensGene.LENGTH0.0760.0040.083
taeGut1.geneSymbol.LENGTH0.0080.0000.011
taeGut1.genscan.LENGTH0.0520.0200.073
taeGut1.nscanGene.LENGTH0.0400.0160.054
taeGut1.refGene.LENGTH0.0120.0000.011
taeGut1.xenoRefGene.LENGTH0.4640.0160.481
tetNig1.ensGene.LENGTH0.1000.0320.130
tetNig1.geneid.LENGTH0.0800.0120.094
tetNig1.genscan.LENGTH0.0960.0120.107
tetNig1.nscanGene.LENGTH0.3370.0160.354
tetNig2.ensGene.LENGTH0.0840.0160.100
unfactor0.0040.0000.005
xenTro1.genscan.LENGTH0.1120.0000.112
xenTro2.ensGene.LENGTH0.1080.0200.126
xenTro2.geneSymbol.LENGTH0.0600.0000.059
xenTro2.genscan.LENGTH0.0800.0440.125
xenTro2.refGene.LENGTH0.0440.0160.057