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Package 31/82HostnameOS / ArchBUILDCHECKBUILD BIN
geneLenDataBase 0.99.5
Matthew Young
Snapshot Date: 2011-02-27 12:29:13 -0800 (Sun, 27 Feb 2011)
URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/geneLenDataBase
Last Changed Rev: 1350 / Revision: 1436
Last Changed Date: 2010-10-13 21:46:15 -0700 (Wed, 13 Oct 2010)
lamb2 Linux (openSUSE 11.2) / x86_64  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  ERROR  ERROR 
pelham Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: geneLenDataBase
Version: 0.99.5
Command: /Library/Frameworks/R.framework/Versions/2.12/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch geneLenDataBase_0.99.5.tar.gz
StartedAt: 2011-02-27 14:42:32 -0800 (Sun, 27 Feb 2011)
EndedAt: 2011-02-27 15:05:23 -0800 (Sun, 27 Feb 2011)
EllapsedTime: 1371.0 seconds
RetCode: 0
Status:  OK 
CheckDir: geneLenDataBase.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.7-data-experiment/meat/geneLenDataBase.Rcheck’
* using R version 2.12.2 Patched (2011-02-25 r54591)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* 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 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 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.LENGTH0.4180.0210.452
anoCar1.genscan.LENGTH0.1150.0140.134
anoCar1.xenoRefGene.LENGTH2.1350.0372.228
anoGam1.ensGene.LENGTH0.1990.0170.217
anoGam1.geneid.LENGTH0.1400.0110.152
anoGam1.genscan.LENGTH0.3100.0110.321
apiMel1.genscan.LENGTH0.0850.0080.097
apiMel2.ensGene.LENGTH0.1740.0140.188
apiMel2.geneid.LENGTH0.1010.0100.112
apiMel2.genscan.LENGTH0.0790.0090.088
aplCal1.xenoRefGene.LENGTH0.9700.0211.003
bosTau2.geneSymbol.LENGTH0.0870.0080.095
bosTau2.geneid.LENGTH1.0200.0261.053
bosTau2.genscan.LENGTH0.2260.0140.254
bosTau2.refGene.LENGTH0.3460.0100.363
bosTau2.sgpGene.LENGTH0.2300.0140.244
bosTau3.ensGene.LENGTH0.2910.0200.317
bosTau3.geneSymbol.LENGTH0.0890.0090.099
bosTau3.geneid.LENGTH0.2610.0180.289
bosTau3.genscan.LENGTH0.2280.0150.250
bosTau3.refGene.LENGTH0.0870.0080.095
bosTau3.sgpGene.LENGTH0.2210.0180.240
bosTau4.ensGene.LENGTH0.2180.0120.232
bosTau4.geneSymbol.LENGTH0.1130.0080.134
bosTau4.genscan.LENGTH0.1590.0120.174
bosTau4.nscanGene.LENGTH0.1420.0070.151
bosTau4.refGene.LENGTH0.0670.0070.077
braFlo1.xenoRefGene.LENGTH1.1800.0231.255
caeJap1.xenoRefGene.LENGTH0.6690.0170.717
caePb1.xenoRefGene.LENGTH0.9080.0200.933
caePb2.xenoRefGene.LENGTH0.8910.0190.911
caeRem2.xenoRefGene.LENGTH0.8160.0190.844
caeRem3.xenoRefGene.LENGTH0.7240.0170.766
calJac1.genscan.LENGTH0.2590.0140.273
calJac1.nscanGene.LENGTH0.2190.0150.243
calJac1.xenoRefGene.LENGTH1.8540.0261.888
canFam1.ensGene.LENGTH0.2150.0110.229
canFam1.geneSymbol.LENGTH0.0130.0020.015
canFam1.genscan.LENGTH0.1440.0120.156
canFam1.nscanGene.LENGTH0.1850.0130.199
canFam1.refGene.LENGTH0.0130.0020.015
canFam1.xenoRefGene.LENGTH1.4960.0221.530
canFam2.ensGene.LENGTH0.1960.0130.222
canFam2.geneSymbol.LENGTH0.0130.0020.015
canFam2.genscan.LENGTH0.1460.0140.169
canFam2.nscanGene.LENGTH0.1430.0120.155
canFam2.refGene.LENGTH0.0130.0020.015
canFam2.xenoRefGene.LENGTH1.2460.0241.291
cavPor3.ensGene.LENGTH0.5110.0210.538
cavPor3.genscan.LENGTH0.2100.0120.232
cavPor3.nscanGene.LENGTH0.1360.0120.148
cavPor3.xenoRefGene.LENGTH1.1290.0201.157
cb1.xenoRefGene.LENGTH0.9140.0200.952
cb3.xenoRefGene.LENGTH0.6620.0160.696
ce2.geneSymbol.LENGTH0.1540.0160.171
ce2.geneid.LENGTH0.1310.0120.144
ce2.refGene.LENGTH0.2040.0150.221
ce4.geneSymbol.LENGTH0.1430.0130.158
ce4.refGene.LENGTH0.1330.0130.160
ce4.xenoRefGene.LENGTH0.1620.0150.183
ce6.ensGene.LENGTH0.1880.0140.205
ce6.geneSymbol.LENGTH0.1390.0120.152
ce6.refGene.LENGTH0.2700.0140.287
ce6.xenoRefGene.LENGTH0.1610.0130.181
ci1.geneSymbol.LENGTH0.0130.0010.015
ci1.refGene.LENGTH0.0120.0010.014
ci1.xenoRefGene.LENGTH0.3900.0160.407
ci2.ensGene.LENGTH0.1550.0170.173
ci2.geneSymbol.LENGTH0.0140.0020.016
ci2.refGene.LENGTH0.0120.0020.014
ci2.xenoRefGene.LENGTH0.7300.0200.764
danRer3.ensGene.LENGTH0.2980.0160.316
danRer3.geneSymbol.LENGTH0.1140.0100.124
danRer3.refGene.LENGTH0.1080.0090.123
danRer4.ensGene.LENGTH0.2560.0150.271
danRer4.geneSymbol.LENGTH0.1130.0100.124
danRer4.genscan.LENGTH0.5330.0140.549
danRer4.nscanGene.LENGTH0.2100.0150.226
danRer4.refGene.LENGTH0.1420.0130.155
danRer5.ensGene.LENGTH0.2900.0160.307
danRer5.geneSymbol.LENGTH0.1180.0120.130
danRer5.refGene.LENGTH0.0910.0090.100
danRer5.vegaGene.LENGTH0.1010.0100.113
danRer5.vegaPseudoGene.LENGTH0.0080.0010.010
danRer6.ensGene.LENGTH0.2330.0130.262
danRer6.geneSymbol.LENGTH0.1160.0120.129
danRer6.refGene.LENGTH0.0960.0090.107
danRer6.xenoRefGene.LENGTH1.0980.0211.124
dm1.geneSymbol.LENGTH0.1340.0140.148
dm1.genscan.LENGTH0.0670.0090.077
dm1.refGene.LENGTH0.1250.0130.138
dm2.geneSymbol.LENGTH0.1300.0110.146
dm2.geneid.LENGTH0.0940.0090.103
dm2.genscan.LENGTH0.1390.0090.148
dm2.nscanGene.LENGTH0.1130.0150.129
dm2.refGene.LENGTH0.1240.0140.139
dm3.geneSymbol.LENGTH0.1420.0130.162
dm3.nscanPasaGene.LENGTH0.2490.0120.261
dm3.refGene.LENGTH0.1360.0130.150
downloadLengthFromUCSC57.359 2.46873.142
dp2.genscan.LENGTH0.0830.0100.125
dp2.xenoRefGene.LENGTH0.4790.0170.498
dp3.geneid.LENGTH0.1100.0120.123
dp3.genscan.LENGTH0.0730.0080.088
dp3.xenoRefGene.LENGTH0.2360.0170.270
droAna1.geneid.LENGTH0.1590.0120.172
droAna1.genscan.LENGTH0.0640.0080.073
droAna1.xenoRefGene.LENGTH0.4340.0170.460
droAna2.genscan.LENGTH0.1240.0150.139
droAna2.xenoRefGene.LENGTH0.6100.0190.633
droEre1.genscan.LENGTH0.0780.0090.088
droEre1.xenoRefGene.LENGTH0.5680.0170.597
droGri1.genscan.LENGTH0.2690.0140.285
droGri1.xenoRefGene.LENGTH0.6170.0180.681
droMoj1.geneid.LENGTH0.4830.0190.503
droMoj1.genscan.LENGTH0.1310.0140.153
droMoj1.xenoRefGene.LENGTH0.4730.0170.494
droMoj2.genscan.LENGTH0.0910.0110.102
droMoj2.xenoRefGene.LENGTH0.6070.0170.631
droPer1.genscan.LENGTH0.0980.0100.108
droPer1.xenoRefGene.LENGTH0.6280.0170.645
droSec1.genscan.LENGTH0.3420.0130.360
droSec1.xenoRefGene.LENGTH0.6360.0180.673
droSim1.geneid.LENGTH0.0990.0100.123
droSim1.genscan.LENGTH0.0660.0070.075
droSim1.xenoRefGene.LENGTH0.5440.0170.580
droVir1.geneid.LENGTH0.2320.0130.248
droVir1.genscan.LENGTH0.1120.0140.159
droVir1.xenoRefGene.LENGTH0.5670.0200.593
droVir2.genscan.LENGTH0.0910.0100.110
droVir2.xenoRefGene.LENGTH0.6100.0160.628
droYak1.geneid.LENGTH0.1050.0110.127
droYak1.genscan.LENGTH0.0770.0080.085
droYak1.xenoRefGene.LENGTH0.5030.0150.519
droYak2.genscan.LENGTH0.0740.0080.089
droYak2.xenoRefGene.LENGTH0.5730.0160.589
equCab1.geneSymbol.LENGTH0.0130.0020.015
equCab1.geneid.LENGTH0.1870.0120.199
equCab1.nscanGene.LENGTH0.0950.0080.104
equCab1.refGene.LENGTH0.0120.0010.014
equCab1.sgpGene.LENGTH0.1490.0120.167
equCab2.ensGene.LENGTH0.2070.0120.221
equCab2.geneSymbol.LENGTH0.0160.0020.019
equCab2.nscanGene.LENGTH0.1170.0100.127
equCab2.refGene.LENGTH0.0160.0020.018
equCab2.xenoRefGene.LENGTH1.1490.0251.193
felCat3.ensGene.LENGTH0.2490.0160.266
felCat3.geneSymbol.LENGTH0.0100.0010.012
felCat3.geneid.LENGTH1.3040.0491.381
felCat3.genscan.LENGTH0.2720.0180.291
felCat3.nscanGene.LENGTH0.6580.0230.682
felCat3.refGene.LENGTH0.0100.0010.012
felCat3.sgpGene.LENGTH0.3220.0150.340
felCat3.xenoRefGene.LENGTH2.2670.0352.314
fr1.ensGene.LENGTH0.1740.0140.190
fr1.genscan.LENGTH0.1380.0120.174
fr2.ensGene.LENGTH0.2790.0130.293
galGal2.ensGene.LENGTH0.1290.0150.144
galGal2.geneSymbol.LENGTH0.0350.0040.053
galGal2.geneid.LENGTH0.1000.0090.111
galGal2.genscan.LENGTH0.1360.0130.150
galGal2.refGene.LENGTH0.0350.0030.039
galGal2.sgpGene.LENGTH0.1060.0100.121
galGal3.ensGene.LENGTH0.1550.0120.168
galGal3.geneSymbol.LENGTH0.0350.0040.056
galGal3.genscan.LENGTH0.1210.0120.134
galGal3.nscanGene.LENGTH0.1490.0130.162
galGal3.refGene.LENGTH0.0320.0030.036
galGal3.xenoRefGene.LENGTH0.9500.0180.973
gasAcu1.ensGene.LENGTH0.1980.0130.212
gasAcu1.nscanGene.LENGTH0.5110.0170.532
hg16.acembly.LENGTH0.8070.0250.835
hg16.ensGene.LENGTH0.1640.0140.179
hg16.exoniphy.LENGTH1.5610.0391.607
hg16.geneSymbol.LENGTH0.2030.0150.224
hg16.geneid.LENGTH0.1260.0130.147
hg16.genscan.LENGTH0.1510.0170.171
hg16.knownGene.LENGTH1.0910.0231.123
hg16.refGene.LENGTH0.1820.0130.197
hg16.sgpGene.LENGTH0.1400.0130.155
hg17.acembly.LENGTH0.8690.0210.898
hg17.acescan.LENGTH0.0240.0030.027
hg17.ccdsGene.LENGTH0.0570.0060.063
hg17.ensGene.LENGTH0.2080.0120.222
hg17.exoniphy.LENGTH0.7620.0210.799
hg17.geneSymbol.LENGTH0.1860.0140.201
hg17.geneid.LENGTH0.1570.0130.170
hg17.genscan.LENGTH0.1410.0130.161
hg17.knownGene.LENGTH0.2290.0150.247
hg17.refGene.LENGTH0.1800.0120.193
hg17.sgpGene.LENGTH0.1560.0120.184
hg17.vegaGene.LENGTH0.0960.0100.108
hg17.vegaPseudoGene.LENGTH0.0400.0060.046
hg17.xenoRefGene.LENGTH0.4190.0200.443
hg18.acembly.LENGTH0.9760.0261.020
hg18.acescan.LENGTH0.0240.0030.027
hg18.ccdsGene.LENGTH0.0790.0080.088
hg18.ensGene.LENGTH0.3620.0170.381
hg18.exoniphy.LENGTH0.8850.0230.926
hg18.geneSymbol.LENGTH0.1920.0140.206
hg18.geneid.LENGTH0.1630.0130.183
hg18.genscan.LENGTH0.1460.0130.161
hg18.knownGene.LENGTH0.3050.0140.331
hg18.knownGeneOld3.LENGTH0.1670.0120.181
hg18.refGene.LENGTH0.1910.0120.203
hg18.sgpGene.LENGTH0.1730.0140.192
hg18.sibGene.LENGTH1.1060.0261.138
hg18.xenoRefGene.LENGTH0.6720.0190.696
hg19.ccdsGene.LENGTH0.0940.0090.104
hg19.ensGene.LENGTH0.5700.0140.585
hg19.exoniphy.LENGTH0.8040.0200.831
hg19.geneSymbol.LENGTH0.1940.0130.207
hg19.knownGene.LENGTH0.3450.0140.359
hg19.nscanGene.LENGTH0.6100.0170.636
hg19.refGene.LENGTH0.1850.0120.198
hg19.xenoRefGene.LENGTH0.6860.0160.706
loxAfr3.xenoRefGene.LENGTH1.5490.0271.584
mm7.ensGene.LENGTH1.0110.0191.037
mm7.geneSymbol.LENGTH0.2070.0170.232
mm7.geneid.LENGTH0.1820.0200.221
mm7.genscan.LENGTH0.1750.0130.190
mm7.knownGene.LENGTH0.1940.0140.225
mm7.refGene.LENGTH0.1710.0120.184
mm7.sgpGene.LENGTH0.1920.0160.210
mm7.xenoRefGene.LENGTH0.6820.0190.717
mm8.ccdsGene.LENGTH0.0590.0070.066
mm8.ensGene.LENGTH0.1760.0130.197
mm8.geneSymbol.LENGTH0.1690.0160.186
mm8.geneid.LENGTH0.1770.0130.191
mm8.genscan.LENGTH0.1500.0130.164
mm8.knownGene.LENGTH0.1840.0130.215
mm8.nscanGene.LENGTH0.8790.0170.929
mm8.refGene.LENGTH0.1560.0130.196
mm8.sgpGene.LENGTH0.1700.0130.197
mm8.sibGene.LENGTH0.5150.0160.549
mm8.xenoRefGene.LENGTH0.6640.0180.707
mm9.acembly.LENGTH0.6370.0180.662
mm9.ccdsGene.LENGTH0.0710.0070.078
mm9.ensGene.LENGTH0.2770.0120.291
mm9.exoniphy.LENGTH0.8360.0180.856
mm9.geneSymbol.LENGTH0.1660.0120.180
mm9.geneid.LENGTH0.1770.0120.193
mm9.genscan.LENGTH0.1500.0140.165
mm9.knownGene.LENGTH0.2210.0170.241
mm9.nscanGene.LENGTH0.1400.0160.167
mm9.refGene.LENGTH0.1590.0130.192
mm9.sgpGene.LENGTH0.1780.0120.191
mm9.xenoRefGene.LENGTH0.6890.0190.721
monDom1.genscan.LENGTH0.1460.0120.177
monDom4.ensGene.LENGTH0.1540.0120.167
monDom4.geneSymbol.LENGTH0.0090.0020.011
monDom4.genscan.LENGTH0.1250.0120.143
monDom4.nscanGene.LENGTH0.1180.0130.134
monDom4.refGene.LENGTH0.0090.0010.011
monDom4.xenoRefGene.LENGTH0.7390.0180.759
monDom5.ensGene.LENGTH0.2260.0120.239
monDom5.geneSymbol.LENGTH0.0100.0010.012
monDom5.genscan.LENGTH0.1230.0130.136
monDom5.nscanGene.LENGTH0.2190.0120.231
monDom5.refGene.LENGTH0.0090.0020.011
monDom5.xenoRefGene.LENGTH1.4540.0331.504
ornAna1.ensGene.LENGTH0.1960.0130.214
ornAna1.geneSymbol.LENGTH0.0070.0010.008
ornAna1.refGene.LENGTH0.0070.0010.008
ornAna1.xenoRefGene.LENGTH1.0170.0201.054
oryLat2.ensGene.LENGTH0.1630.0120.175
oryLat2.geneSymbol.LENGTH0.0100.0020.012
oryLat2.refGene.LENGTH0.0110.0010.012
oryLat2.xenoRefGene.LENGTH0.9120.0190.932
panTro1.ensGene.LENGTH0.2120.0120.224
panTro1.geneid.LENGTH0.1220.0120.135
panTro1.genscan.LENGTH0.1640.0140.178
panTro1.xenoRefGene.LENGTH0.2700.0180.288
panTro2.ensGene.LENGTH0.2550.0140.325
panTro2.geneSymbol.LENGTH0.1960.0140.212
panTro2.genscan.LENGTH0.1440.0140.159
panTro2.nscanGene.LENGTH0.1330.0130.148
panTro2.refGene.LENGTH0.2020.0140.218
panTro2.xenoRefGene.LENGTH0.9310.0231.009
petMar1.xenoRefGene.LENGTH0.5110.0170.532
ponAbe2.ensGene.LENGTH0.1810.0120.194
ponAbe2.geneSymbol.LENGTH0.0280.0030.031
ponAbe2.genscan.LENGTH0.3780.0170.401
ponAbe2.nscanGene.LENGTH0.1340.0130.149
ponAbe2.refGene.LENGTH0.0260.0030.031
ponAbe2.xenoRefGene.LENGTH1.2040.0221.279
priPac1.xenoRefGene.LENGTH0.7230.0170.749
rheMac2.ensGene.LENGTH0.3010.0160.320
rheMac2.geneSymbol.LENGTH0.0130.0010.014
rheMac2.geneid.LENGTH0.1550.0110.166
rheMac2.nscanGene.LENGTH0.1320.0150.148
rheMac2.refGene.LENGTH0.0130.0020.014
rheMac2.sgpGene.LENGTH0.1540.0140.169
rheMac2.xenoRefGene.LENGTH0.9930.0201.037
rn3.ensGene.LENGTH0.8420.0180.863
rn3.geneSymbol.LENGTH0.1140.0080.123
rn3.geneid.LENGTH0.1280.0120.141
rn3.genscan.LENGTH0.1650.0150.191
rn3.knownGene.LENGTH0.0500.0040.055
rn3.nscanGene.LENGTH0.1270.0120.140
rn3.refGene.LENGTH0.1020.0090.115
rn3.sgpGene.LENGTH0.1400.0120.154
rn3.xenoRefGene.LENGTH1.1150.0231.143
rn4.ensGene.LENGTH0.2900.0140.312
rn4.geneSymbol.LENGTH0.1040.0090.115
rn4.geneid.LENGTH0.1880.0140.202
rn4.genscan.LENGTH0.1460.0130.164
rn4.knownGene.LENGTH0.0520.0060.059
rn4.nscanGene.LENGTH0.1280.0130.144
rn4.refGene.LENGTH0.1040.0100.116
rn4.sgpGene.LENGTH0.1750.0130.192
rn4.xenoRefGene.LENGTH1.5580.0251.593
sacCer1.ensGene.LENGTH0.0420.0040.047
sacCer2.ensGene.LENGTH0.0410.0040.045
strPur1.geneSymbol.LENGTH0.0110.0020.013
strPur1.genscan.LENGTH0.1890.0150.209
strPur1.refGene.LENGTH0.0110.0010.013
strPur1.xenoRefGene.LENGTH1.0620.0201.088
strPur2.geneSymbol.LENGTH0.0100.0020.012
strPur2.genscan.LENGTH0.2440.0170.264
strPur2.refGene.LENGTH0.0100.0020.012
strPur2.xenoRefGene.LENGTH1.2410.0261.273
supportedGeneIDs0.0270.0020.028
supportedGenomes0.0850.0060.135
taeGut1.ensGene.LENGTH0.1240.0110.137
taeGut1.geneSymbol.LENGTH0.0070.0010.009
taeGut1.genscan.LENGTH0.0790.0080.087
taeGut1.nscanGene.LENGTH0.0580.0050.070
taeGut1.refGene.LENGTH0.0070.0010.008
taeGut1.xenoRefGene.LENGTH0.8350.0190.856
tetNig1.ensGene.LENGTH0.1920.0130.207
tetNig1.geneid.LENGTH0.1480.0130.162
tetNig1.genscan.LENGTH0.1150.0130.131
tetNig1.nscanGene.LENGTH0.1520.0120.165
tetNig2.ensGene.LENGTH0.1450.0140.159
unfactor0.0110.0020.016
xenTro1.genscan.LENGTH0.1910.0160.218
xenTro2.ensGene.LENGTH0.1690.0120.193
xenTro2.geneSymbol.LENGTH0.0630.0060.069
xenTro2.genscan.LENGTH0.1730.0130.191
xenTro2.refGene.LENGTH0.0640.0070.075