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Package 31/84HostnameOS / ArchBUILDCHECKBUILD BIN
geneLenDataBase 0.99.5
Matthew Young
Snapshot Date: 2010-11-12 00:25:07 -0800 (Fri, 12 Nov 2010)
URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/geneLenDataBase
Last Changed Rev: 1350 / Revision: 1384
Last Changed Date: 2010-10-13 21:46:15 -0700 (Wed, 13 Oct 2010)
lamb1 Linux (openSUSE 11.3) / 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: 0.99.5
Command: E:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings geneLenDataBase_0.99.5.tar.gz
StartedAt: 2010-11-12 03:50:41 -0800 (Fri, 12 Nov 2010)
EndedAt: 2010-11-12 04:13:05 -0800 (Fri, 12 Nov 2010)
EllapsedTime: 1343.5 seconds
RetCode: 0
Status:  OK  
CheckDir: geneLenDataBase.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.8-data-experiment/meat/geneLenDataBase.Rcheck'
* using R version 2.13.0 Under development (unstable) (2010-11-10 r53547)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'geneLenDataBase/DESCRIPTION' ... OK
* this is package 'geneLenDataBase' version '0.99.5'
* 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 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 for unstated dependencies in examples ... OK
* checking data for non-ASCII characters ... OK
* checking examples ... OK
* checking PDF version of manual ... OK

geneLenDataBase.Rcheck/00install.out:

* 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.LENGTH0.150.040.25
anoCar1.genscan.LENGTH0.140.040.29
anoCar1.xenoRefGene.LENGTH1.970.112.22
anoGam1.ensGene.LENGTH0.190.030.21
anoGam1.geneid.LENGTH0.110.090.20
anoGam1.genscan.LENGTH0.090.100.19
apiMel1.genscan.LENGTH0.300.040.36
apiMel2.ensGene.LENGTH0.160.030.20
apiMel2.geneid.LENGTH0.120.050.18
apiMel2.genscan.LENGTH0.090.050.14
aplCal1.xenoRefGene.LENGTH0.700.120.83
bosTau2.geneSymbol.LENGTH0.110.050.16
bosTau2.geneid.LENGTH0.490.020.50
bosTau2.genscan.LENGTH0.360.110.57
bosTau2.refGene.LENGTH0.110.030.14
bosTau2.sgpGene.LENGTH0.430.030.47
bosTau3.ensGene.LENGTH0.190.060.25
bosTau3.geneSymbol.LENGTH0.060.060.14
bosTau3.geneid.LENGTH0.210.050.25
bosTau3.genscan.LENGTH0.200.080.28
bosTau3.refGene.LENGTH0.080.040.13
bosTau3.sgpGene.LENGTH0.140.110.26
bosTau4.ensGene.LENGTH0.190.050.25
bosTau4.geneSymbol.LENGTH0.060.060.12
bosTau4.genscan.LENGTH0.140.050.19
bosTau4.nscanGene.LENGTH0.120.050.17
bosTau4.refGene.LENGTH0.110.010.12
braFlo1.xenoRefGene.LENGTH0.860.100.97
caeJap1.xenoRefGene.LENGTH0.820.010.82
caePb1.xenoRefGene.LENGTH0.750.030.80
caePb2.xenoRefGene.LENGTH0.810.110.94
caeRem2.xenoRefGene.LENGTH0.730.000.75
caeRem3.xenoRefGene.LENGTH0.670.030.72
calJac1.genscan.LENGTH0.210.080.28
calJac1.nscanGene.LENGTH0.230.010.25
calJac1.xenoRefGene.LENGTH1.530.001.55
canFam1.ensGene.LENGTH0.170.030.20
canFam1.geneSymbol.LENGTH0.020.020.03
canFam1.genscan.LENGTH0.160.050.22
canFam1.nscanGene.LENGTH0.150.030.19
canFam1.refGene.LENGTH0.020.000.01
canFam1.xenoRefGene.LENGTH1.140.101.23
canFam2.ensGene.LENGTH0.190.040.24
canFam2.geneSymbol.LENGTH0.010.000.01
canFam2.genscan.LENGTH0.190.050.23
canFam2.nscanGene.LENGTH0.080.060.14
canFam2.refGene.LENGTH0.010.000.02
canFam2.xenoRefGene.LENGTH1.050.081.12
cavPor3.ensGene.LENGTH0.140.030.17
cavPor3.genscan.LENGTH0.250.070.31
cavPor3.nscanGene.LENGTH0.200.040.25
cavPor3.xenoRefGene.LENGTH1.020.111.15
cb1.xenoRefGene.LENGTH0.810.020.82
cb3.xenoRefGene.LENGTH0.500.010.60
ce2.geneSymbol.LENGTH0.170.080.25
ce2.geneid.LENGTH0.110.000.11
ce2.refGene.LENGTH0.140.110.25
ce4.geneSymbol.LENGTH0.110.130.23
ce4.refGene.LENGTH0.120.110.24
ce4.xenoRefGene.LENGTH0.180.000.17
ce6.ensGene.LENGTH0.150.040.21
ce6.geneSymbol.LENGTH0.100.130.43
ce6.refGene.LENGTH0.100.120.22
ce6.xenoRefGene.LENGTH0.100.030.14
ci1.geneSymbol.LENGTH0.040.000.03
ci1.refGene.LENGTH0.000.020.02
ci1.xenoRefGene.LENGTH0.310.000.31
ci2.ensGene.LENGTH0.150.000.15
ci2.geneSymbol.LENGTH0.000.030.04
ci2.refGene.LENGTH0.020.000.01
ci2.xenoRefGene.LENGTH0.590.060.66
danRer3.ensGene.LENGTH0.160.080.23
danRer3.geneSymbol.LENGTH0.050.130.17
danRer3.refGene.LENGTH0.340.030.37
danRer4.ensGene.LENGTH0.170.050.22
danRer4.geneSymbol.LENGTH0.130.050.17
danRer4.genscan.LENGTH0.150.010.17
danRer4.nscanGene.LENGTH0.190.050.24
danRer4.refGene.LENGTH0.060.090.17
danRer5.ensGene.LENGTH0.190.000.20
danRer5.geneSymbol.LENGTH0.080.070.14
danRer5.refGene.LENGTH0.060.080.14
danRer5.vegaGene.LENGTH0.160.030.19
danRer5.vegaPseudoGene.LENGTH0.010.000.02
danRer6.ensGene.LENGTH0.180.080.25
danRer6.geneSymbol.LENGTH0.090.060.15
danRer6.refGene.LENGTH0.060.060.16
danRer6.xenoRefGene.LENGTH0.920.111.03
dm1.geneSymbol.LENGTH0.140.080.22
dm1.genscan.LENGTH0.300.060.50
dm1.refGene.LENGTH0.080.130.20
dm2.geneSymbol.LENGTH0.120.110.24
dm2.geneid.LENGTH0.080.060.14
dm2.genscan.LENGTH0.080.030.12
dm2.nscanGene.LENGTH0.080.020.10
dm2.refGene.LENGTH0.110.090.20
dm3.geneSymbol.LENGTH0.090.020.11
dm3.nscanPasaGene.LENGTH0.080.100.17
dm3.refGene.LENGTH0.110.010.12
downloadLengthFromUCSC 50.16 0.78100.41
dp2.genscan.LENGTH0.040.080.19
dp2.xenoRefGene.LENGTH0.360.090.58
dp3.geneid.LENGTH0.090.070.18
dp3.genscan.LENGTH0.060.040.19
dp3.xenoRefGene.LENGTH0.180.130.41
droAna1.geneid.LENGTH0.140.010.37
droAna1.genscan.LENGTH0.040.080.19
droAna1.xenoRefGene.LENGTH0.330.110.55
droAna2.genscan.LENGTH0.110.020.45
droAna2.xenoRefGene.LENGTH0.550.040.71
droEre1.genscan.LENGTH0.080.070.56
droEre1.xenoRefGene.LENGTH0.510.140.78
droGri1.genscan.LENGTH0.110.080.29
droGri1.xenoRefGene.LENGTH0.580.010.71
droMoj1.geneid.LENGTH0.690.050.86
droMoj1.genscan.LENGTH0.140.000.20
droMoj1.xenoRefGene.LENGTH0.400.120.67
droMoj2.genscan.LENGTH0.090.050.22
droMoj2.xenoRefGene.LENGTH0.470.170.76
droPer1.genscan.LENGTH0.110.080.25
droPer1.xenoRefGene.LENGTH0.550.130.77
droSec1.genscan.LENGTH0.030.070.21
droSec1.xenoRefGene.LENGTH0.550.000.65
droSim1.geneid.LENGTH0.070.080.22
droSim1.genscan.LENGTH0.070.060.19
droSim1.xenoRefGene.LENGTH0.420.050.58
droVir1.geneid.LENGTH0.200.010.40
droVir1.genscan.LENGTH0.080.080.23
droVir1.xenoRefGene.LENGTH0.800.081.08
droVir2.genscan.LENGTH0.110.050.24
droVir2.xenoRefGene.LENGTH0.590.070.78
droYak1.geneid.LENGTH0.090.100.25
droYak1.genscan.LENGTH0.050.110.21
droYak1.xenoRefGene.LENGTH0.420.020.53
droYak2.genscan.LENGTH0.110.010.17
droYak2.xenoRefGene.LENGTH0.530.100.77
equCab1.geneSymbol.LENGTH0.020.000.07
equCab1.geneid.LENGTH0.150.080.30
equCab1.nscanGene.LENGTH0.080.060.36
equCab1.refGene.LENGTH0.020.010.08
equCab1.sgpGene.LENGTH0.150.020.26
equCab2.ensGene.LENGTH0.150.090.34
equCab2.geneSymbol.LENGTH0.030.000.05
equCab2.nscanGene.LENGTH0.140.080.26
equCab2.refGene.LENGTH0.000.020.03
equCab2.xenoRefGene.LENGTH0.920.041.11
felCat3.ensGene.LENGTH0.180.000.23
felCat3.geneSymbol.LENGTH0.000.000.01
felCat3.geneid.LENGTH1.230.051.72
felCat3.genscan.LENGTH0.200.080.34
felCat3.nscanGene.LENGTH0.210.030.30
felCat3.refGene.LENGTH0.010.000.05
felCat3.sgpGene.LENGTH0.200.030.30
felCat3.xenoRefGene.LENGTH1.780.092.33
fr1.ensGene.LENGTH0.140.080.97
fr1.genscan.LENGTH0.100.030.39
fr2.ensGene.LENGTH1.000.061.17
galGal2.ensGene.LENGTH0.090.000.56
galGal2.geneSymbol.LENGTH0.030.030.10
galGal2.geneid.LENGTH0.060.080.25
galGal2.genscan.LENGTH0.150.080.31
galGal2.refGene.LENGTH0.030.010.08
galGal2.sgpGene.LENGTH0.070.110.25
galGal3.ensGene.LENGTH0.110.030.88
galGal3.geneSymbol.LENGTH0.040.020.08
galGal3.genscan.LENGTH0.070.120.62
galGal3.nscanGene.LENGTH0.120.000.61
galGal3.refGene.LENGTH0.040.030.51
galGal3.xenoRefGene.LENGTH0.760.021.00
gasAcu1.ensGene.LENGTH0.110.111.22
gasAcu1.nscanGene.LENGTH0.830.091.00
hg16.acembly.LENGTH0.590.050.89
hg16.ensGene.LENGTH0.110.060.93
hg16.exoniphy.LENGTH0.410.040.81
hg16.geneSymbol.LENGTH0.170.040.24
hg16.geneid.LENGTH0.120.090.77
hg16.genscan.LENGTH0.160.020.72
hg16.knownGene.LENGTH0.200.060.47
hg16.refGene.LENGTH0.120.031.03
hg16.sgpGene.LENGTH0.100.050.23
hg17.acembly.LENGTH0.610.051.27
hg17.acescan.LENGTH0.010.010.27
hg17.ccdsGene.LENGTH0.050.050.39
hg17.ensGene.LENGTH0.170.060.64
hg17.exoniphy.LENGTH0.600.102.81
hg17.geneSymbol.LENGTH0.170.030.94
hg17.geneid.LENGTH0.110.080.52
hg17.genscan.LENGTH0.170.030.23
hg17.knownGene.LENGTH0.160.080.30
hg17.refGene.LENGTH0.210.010.50
hg17.sgpGene.LENGTH0.140.050.97
hg17.vegaGene.LENGTH0.100.032.62
hg17.vegaPseudoGene.LENGTH0.010.010.11
hg17.xenoRefGene.LENGTH0.300.061.11
hg18.acembly.LENGTH0.750.052.75
hg18.acescan.LENGTH0.020.020.19
hg18.ccdsGene.LENGTH0.090.031.10
hg18.ensGene.LENGTH0.300.061.45
hg18.exoniphy.LENGTH1.080.142.83
hg18.geneSymbol.LENGTH0.150.050.96
hg18.geneid.LENGTH0.170.030.98
hg18.genscan.LENGTH0.130.040.64
hg18.knownGene.LENGTH0.220.081.14
hg18.knownGeneOld3.LENGTH0.140.070.49
hg18.refGene.LENGTH0.150.030.55
hg18.sgpGene.LENGTH0.130.060.22
hg18.sibGene.LENGTH0.590.100.84
hg18.xenoRefGene.LENGTH0.530.080.72
hg19.ccdsGene.LENGTH0.110.030.19
hg19.ensGene.LENGTH0.500.080.62
hg19.exoniphy.LENGTH0.730.100.94
hg19.geneSymbol.LENGTH0.130.060.30
hg19.knownGene.LENGTH0.650.060.78
hg19.nscanGene.LENGTH0.250.030.32
hg19.refGene.LENGTH0.190.030.25
hg19.xenoRefGene.LENGTH0.550.030.74
loxAfr3.xenoRefGene.LENGTH1.140.021.30
mm7.ensGene.LENGTH0.810.020.87
mm7.geneSymbol.LENGTH0.140.010.21
mm7.geneid.LENGTH0.110.050.25
mm7.genscan.LENGTH0.100.060.24
mm7.knownGene.LENGTH0.110.050.51
mm7.refGene.LENGTH0.140.000.17
mm7.sgpGene.LENGTH0.120.060.27
mm7.xenoRefGene.LENGTH0.640.030.72
mm8.ccdsGene.LENGTH0.080.020.12
mm8.ensGene.LENGTH0.170.000.39
mm8.geneSymbol.LENGTH0.140.000.19
mm8.geneid.LENGTH0.140.040.24
mm8.genscan.LENGTH0.130.050.25
mm8.knownGene.LENGTH0.150.030.23
mm8.nscanGene.LENGTH0.100.030.19
mm8.refGene.LENGTH0.140.000.19
mm8.sgpGene.LENGTH0.110.100.26
mm8.sibGene.LENGTH0.400.070.55
mm8.xenoRefGene.LENGTH0.550.110.92
mm9.acembly.LENGTH0.500.070.61
mm9.ccdsGene.LENGTH0.020.090.16
mm9.ensGene.LENGTH0.280.050.47
mm9.exoniphy.LENGTH0.690.080.86
mm9.geneSymbol.LENGTH0.110.010.15
mm9.geneid.LENGTH0.160.060.25
mm9.genscan.LENGTH0.110.050.19
mm9.knownGene.LENGTH0.180.110.45
mm9.nscanGene.LENGTH0.080.030.17
mm9.refGene.LENGTH0.110.020.17
mm9.sgpGene.LENGTH0.160.060.25
mm9.xenoRefGene.LENGTH0.540.090.75
monDom1.genscan.LENGTH0.130.030.22
monDom4.ensGene.LENGTH0.140.050.20
monDom4.geneSymbol.LENGTH0.020.000.01
monDom4.genscan.LENGTH0.100.130.29
monDom4.nscanGene.LENGTH0.130.070.25
monDom4.refGene.LENGTH0.020.000.09
monDom4.xenoRefGene.LENGTH0.600.051.07
monDom5.ensGene.LENGTH0.190.030.26
monDom5.geneSymbol.LENGTH0.000.000.01
monDom5.genscan.LENGTH0.100.020.13
monDom5.nscanGene.LENGTH0.200.010.29
monDom5.refGene.LENGTH0.010.000.03
monDom5.xenoRefGene.LENGTH1.240.131.64
ornAna1.ensGene.LENGTH0.200.060.40
ornAna1.geneSymbol.LENGTH0.030.000.04
ornAna1.refGene.LENGTH0.020.000.01
ornAna1.xenoRefGene.LENGTH0.890.061.31
oryLat2.ensGene.LENGTH0.160.030.27
oryLat2.geneSymbol.LENGTH0.000.000.07
oryLat2.refGene.LENGTH0.010.020.04
oryLat2.xenoRefGene.LENGTH0.780.021.14
panTro1.ensGene.LENGTH0.190.040.30
panTro1.geneid.LENGTH0.160.070.28
panTro1.genscan.LENGTH0.090.050.25
panTro1.xenoRefGene.LENGTH0.230.030.33
panTro2.ensGene.LENGTH0.180.060.33
panTro2.geneSymbol.LENGTH0.170.050.48
panTro2.genscan.LENGTH0.090.060.30
panTro2.nscanGene.LENGTH0.100.030.20
panTro2.refGene.LENGTH0.140.050.34
panTro2.xenoRefGene.LENGTH0.780.061.11
petMar1.xenoRefGene.LENGTH0.450.100.69
ponAbe2.ensGene.LENGTH0.130.090.38
ponAbe2.geneSymbol.LENGTH0.010.030.09
ponAbe2.genscan.LENGTH0.160.020.23
ponAbe2.nscanGene.LENGTH0.090.000.17
ponAbe2.refGene.LENGTH0.020.010.08
ponAbe2.xenoRefGene.LENGTH0.980.011.31
priPac1.xenoRefGene.LENGTH0.550.050.76
rheMac2.ensGene.LENGTH0.500.040.65
rheMac2.geneSymbol.LENGTH0.010.020.04
rheMac2.geneid.LENGTH0.180.010.25
rheMac2.nscanGene.LENGTH0.120.020.22
rheMac2.refGene.LENGTH0.020.000.05
rheMac2.sgpGene.LENGTH0.120.050.24
rheMac2.xenoRefGene.LENGTH0.860.061.12
rn3.ensGene.LENGTH0.140.110.36
rn3.geneSymbol.LENGTH0.110.080.25
rn3.geneid.LENGTH0.110.030.17
rn3.genscan.LENGTH0.110.060.22
rn3.knownGene.LENGTH0.070.030.12
rn3.nscanGene.LENGTH0.080.000.14
rn3.refGene.LENGTH0.100.060.22
rn3.sgpGene.LENGTH0.680.020.76
rn3.xenoRefGene.LENGTH0.860.111.18
rn4.ensGene.LENGTH0.210.060.37
rn4.geneSymbol.LENGTH0.100.060.20
rn4.geneid.LENGTH0.150.080.44
rn4.genscan.LENGTH0.070.080.80
rn4.knownGene.LENGTH0.050.030.14
rn4.nscanGene.LENGTH0.140.090.28
rn4.refGene.LENGTH0.130.050.27
rn4.sgpGene.LENGTH0.090.110.31
rn4.xenoRefGene.LENGTH0.580.131.92
sacCer1.ensGene.LENGTH0.030.040.12
sacCer2.ensGene.LENGTH0.010.050.14
strPur1.geneSymbol.LENGTH0.040.000.05
strPur1.genscan.LENGTH0.170.080.33
strPur1.refGene.LENGTH0.000.010.03
strPur1.xenoRefGene.LENGTH0.830.081.04
strPur2.geneSymbol.LENGTH0.010.000.04
strPur2.genscan.LENGTH0.220.030.32
strPur2.refGene.LENGTH0.020.000.05
strPur2.xenoRefGene.LENGTH0.950.071.19
supportedGeneIDs0.010.000.03
supportedGenomes0.680.000.83
taeGut1.ensGene.LENGTH0.090.010.22
taeGut1.geneSymbol.LENGTH0.000.000.01
taeGut1.genscan.LENGTH0.060.080.19
taeGut1.nscanGene.LENGTH0.060.050.14
taeGut1.refGene.LENGTH0.000.000.02
taeGut1.xenoRefGene.LENGTH0.610.041.06
tetNig1.ensGene.LENGTH0.130.080.33
tetNig1.geneid.LENGTH0.100.050.22
tetNig1.genscan.LENGTH0.130.040.24
tetNig1.nscanGene.LENGTH0.120.040.27
tetNig2.ensGene.LENGTH0.140.010.20
unfactor0.000.000.03
xenTro1.genscan.LENGTH0.130.020.24
xenTro2.ensGene.LENGTH0.150.040.25
xenTro2.geneSymbol.LENGTH0.050.070.26
xenTro2.genscan.LENGTH0.120.110.29
xenTro2.refGene.LENGTH0.080.030.14