- using R version 3.0.1 (2013-05-16)
- using platform: i686-pc-linux-gnu (32-bit)
- using session charset: UTF-8
- checking for file ‘supclust/DESCRIPTION’ ... OK
- this is package ‘supclust’ version ‘1.0-7’
- package encoding: UTF-8
- 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 executable files ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking whether package ‘supclust’ can be installed ... OK
- checking installed package size ... OK
- checking package 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
- 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 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 ... NOTE
.p.1gen: warning in formatC(id, wid = 6): partial argument match of
'wid' to 'width'
.p.1gen: warning in formatC(s, wid = 4): partial argument match of
'wid' to 'width'
.p.1gen: warning in formatC(format(c(round(m, digits = digits),
0.735))[1], wid = 7, dig = 3): partial argument match of 'dig' to
'digits'
.p.1gen: warning in formatC(format(c(round(m, digits = digits),
0.735))[1], wid = 7, dig = 3): partial argument match of 'wid' to
'width'
predict.pelora: warning in matrix(c((1/(1 + exp(-(X[, 1:(noc[i] + 1)]
%*% koeff))))), nc = 1): partial argument match of 'nc' to 'ncol'
ridge.coef: warning in diag(apply(X, 2, var) * lambda * nrow(X), nr =
ncol(X)): partial argument match of 'nr' to 'nrow'
- 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 contents of ‘data’ directory ... OK
- checking data for non-ASCII characters ... OK
- checking data for ASCII and uncompressed saves ... OK
- checking line endings in C/C++/Fortran sources/headers ... OK
- checking line endings in Makefiles ... OK
- checking for portable compilation flags in Makevars ... OK
- checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
- checking compiled code ... OK
- checking examples ... [23s/23s] OK
- checking for unstated dependencies in tests ... OK
- checking tests ... [7s/7s] OK
Running ‘pelora-ex.R’ [5s/6s]
Comparing ‘pelora-ex.Rout’ to ‘pelora-ex.Rout.save’ ... OK
Running ‘wilma-ex.R’ [1s/1s]
Comparing ‘wilma-ex.Rout’ to ‘wilma-ex.Rout.save’ ...207c207
< Gen[5] : 219 Score: 0 Margin: 0.528
---
> Gen[5] : 208 Score: 0 Margin: 0.528
210,216c210
< Gen[8] : 120 Score: 0 Margin: 0.656
< Gen[9] : 120 Score: 0 Margin: 0.656
< Gen[10]: 211 Score: 0 Margin: 0.657
< Gen[11]: 100 Score: 0 Margin: 0.676
< Gen[12]: 56 Score: 0 Margin: 0.686
< Gen[13]: 120 Score: 0 Margin: 0.688
< gic size changed from 0 to 13
---
> gic size changed from 0 to 7
227c221
< Gen: 219 Score: 0 Margin: 0.528
---
> Gen: 208 Score: 0 Margin: 0.528
230,235d223
< Gen: 120 Score: 0 Margin: 0.656
< Gen: 120 Score: 0 Margin: 0.656
< Gen: 211 Score: 0 Margin: 0.657
< Gen: 100 Score: 0 Margin: 0.676
< Gen: 56 Score: 0 Margin: 0.686
< Gen: 120 Score: 0 Margin: 0.688
263,267c251,256
< Gen[1] : 31 Score: 10 Margin: -0.735
< Gen[2] : 215 Score: 0 Margin: 0.253
< Gen[3] : 114 Score: 0 Margin: 0.319
< Gen[4] : 248 Score: 0 Margin: 0.353
< gic size changed from 0 to 4
---
> Gen[1] : 211 Score: 8 Margin: -0.703
> Gen[2] : 8 Score: 0 Margin: 0.080
> Gen[3] : 79 Score: 0 Margin: 0.334
> Gen[4] : 120 Score: 0 Margin: 0.489
> Gen[5] : 61 Score: 0 Margin: 0.501
> gic size changed from 0 to 5
274,277c263,267
< Gen: 31 Score: 10 Margin: -0.735
< Gen: 215 Score: 0 Margin: 0.253
< Gen: 114 Score: 0 Margin: 0.319
< Gen: 248 Score: 0 Margin: 0.353
---
> Gen: 211 Score: 8 Margin: -0.703
> Gen: 8 Score: 0 Margin: 0.080
> Gen: 79 Score: 0 Margin: 0.334
> Gen: 120 Score: 0 Margin: 0.489
> Gen: 61 Score: 0 Margin: 0.501
720c710
< Cluster 3 : Contains 13 genes, final score 0, final margin 0.69
---
> Cluster 3 : Contains 7 genes, final score 0, final margin 0.63
722c712
< Cluster 5 : Contains 4 genes, final score 0, final margin 0.35
---
> Cluster 5 : Contains 5 genes, final score 0, final margin 0.50
755c745
< Gen: 219 Score: 0 Margin: 0.528
---
> Gen: 208 Score: 0 Margin: 0.528
758,763d747
< Gen: 120 Score: 0 Margin: 0.656
< Gen: 120 Score: 0 Margin: 0.656
< Gen: 211 Score: 0 Margin: 0.657
< Gen: 100 Score: 0 Margin: 0.676
< Gen: 56 Score: 0 Margin: 0.686
< Gen: 120 Score: 0 Margin: 0.688
776,779c760,764
< Gen: 31 Score: 10 Margin: -0.735
< Gen: 215 Score: 0 Margin: 0.253
< Gen: 114 Score: 0 Margin: 0.319
< Gen: 248 Score: 0 Margin: 0.353
---
> Gen: 211 Score: 8 Margin: -0.703
> Gen: 8 Score: 0 Margin: 0.080
> Gen: 79 Score: 0 Margin: 0.334
> Gen: 120 Score: 0 Margin: 0.489
> Gen: 61 Score: 0 Margin: 0.501
783,820c768,805
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---
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> 28 1.09049995 0.8301002018 0.71657244 0.2943620 0.52349395
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828,865c813,850
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---
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> 13 -0.70858878 -0.2158745127 -0.33886664 -1.1701397 -0.39219258
> 14 -0.23898252 -0.2019026598 0.05768892 -0.6283926 -0.49487021
> 15 -0.60859571 -0.3180281923 0.01046894 -0.9265950 -0.79493534
> 16 -0.33423842 -0.2871141977 -0.11687460 -0.7639704 -0.72253510
> 17 -0.03841954 -0.0403125083 -0.10227418 -0.5534439 -0.19060863
> 18 -0.59363662 -0.1480612891 0.08273906 -0.6035579 -0.19231797
> 19 -0.10811321 0.0296883498 -0.24693813 -0.4747635 -0.18770935
> 20 -0.12702101 -0.2665362495 -0.11348299 -0.4094214 -0.44598608
> 21 -0.53038176 -0.1294641737 -0.14259505 -0.5126285 -0.49915531
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> 23 -0.32441170 -0.1446490007 -0.31043378 -0.8132257 -0.41305718
> 24 -0.82065665 -0.0639724940 -0.14904600 -0.5758121 -0.23025813
> 25 -0.02893058 0.0066962331 -0.13526013 -0.6085560 -0.27252990
> 26 -0.55089076 -0.1241664201 -0.13370461 -0.9905168 -0.27694500
> 27 -0.86619381 -0.2433286875 -0.05104831 -0.9025096 -0.43696893
> 28 1.09049995 0.8301002018 0.71657244 0.2943620 0.52349395
> 29 1.57469121 0.8368946854 1.49530822 1.5944701 0.52166803
> 30 1.23156260 1.0180481164 1.05258396 0.6200992 0.42090893
> 31 1.10402966 0.8312227078 0.71492310 0.5222981 0.43211687
> 32 1.47675576 0.7598054368 0.79212873 0.3681568 0.44364323
> 33 1.08905787 0.7604573437 1.14743514 0.8893017 0.47322292
> 34 1.06577421 0.9051386177 0.73841857 0.9792604 0.67750897
> 35 0.99636230 0.7940511189 0.91638013 0.3118163 0.41905389
> 36 1.21392809 0.8575998603 0.92296241 0.3266311 0.51187359
> 37 1.46585533 0.8570374764 1.38248424 0.7115797 0.93543524
> 38 1.11997891 0.7987867842 0.76811365 0.3013484 0.42598663
869,871c854,856
< 1 -0.2659565 -0.41967970 0.25420331 0.13213573 -0.7454166
< 2 0.0630622 0.04897851 -0.08651249 -0.36667922 0.1266530
< 3 -0.4861635 -0.15418024 -0.09294546 0.05706068 -0.1871627
---
> 1 -0.2659565 -0.41967970 0.1865981 0.13213573 0.1370108
> 2 0.0630622 0.04897851 -0.8151532 -0.36667922 -0.5859375
> 3 -0.4861635 -0.15418024 0.4980405 0.05706068 -0.9458966
- checking PDF version of manual ... OK
NOTE: There was 1 note.
See
‘/home/hornik/tmp/R.check/r-release/Work/PKGS/supclust.Rcheck/00check.log’
for details.