BioC 2.13: CHECK report for CNAnorm on zin1

Package: CNAnorm

Version: 1.8.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings CNAnorm_1.8.0.tar.gz

StartedAt: 2014-04-05 00:25:54 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 00:26:43 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 49.5 seconds

RetCode: 0

Status:  OK

CheckDir: CNAnorm.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/CNAnorm.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CNAnorm/DESCRIPTION’ ... OK
* this is package ‘CNAnorm’ version ‘1.8.0’
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CNAnorm’ can be installed ... [2s/2s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’
A package should be listed in only one of these fields.
* 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 dependencies in R code ... NOTE
Package in Depends field not imported from: ‘DNAcopy’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 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 use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘CNAnorm.Snw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [25s/25s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
peakPloidy 20.101  0.024  20.177
* 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

NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/CNAnorm.Rcheck/00check.log’
for details.

* installing *source* package ‘CNAnorm’ ...
** libs
gfortran   -fpic  -g -O2  -Wall -c daxpy.f -o daxpy.o
gfortran   -fpic  -g -O2  -Wall -c ddot.f -o ddot.o
gfortran   -fpic  -g -O2  -Wall -c dgbfa.f -o dgbfa.o
gfortran   -fpic  -g -O2  -Wall -c dgbsl.f -o dgbsl.o
gfortran   -fpic  -g -O2  -Wall -c dscal.f -o dscal.o
gfortran   -fpic  -g -O2  -Wall -c dsmooth.f -o dsmooth.o
Warning: Nonconforming tab character in column 1 of line 14
Warning: Nonconforming tab character in column 1 of line 15
Warning: Nonconforming tab character in column 1 of line 16
Warning: Nonconforming tab character in column 1 of line 17
Warning: Nonconforming tab character in column 1 of line 18
Warning: Nonconforming tab character in column 1 of line 19
Warning: Nonconforming tab character in column 1 of line 20
Warning: Nonconforming tab character in column 1 of line 21
Warning: Nonconforming tab character in column 1 of line 22
Warning: Nonconforming tab character in column 3 of line 23
Warning: Nonconforming tab character in column 1 of line 24
Warning: Nonconforming tab character in column 1 of line 25
Warning: Nonconforming tab character in column 1 of line 26
Warning: Nonconforming tab character in column 1 of line 27
Warning: Nonconforming tab character in column 1 of line 28
Warning: Nonconforming tab character in column 1 of line 29
Warning: Nonconforming tab character in column 1 of line 30
Warning: Nonconforming tab character in column 1 of line 31
Warning: Nonconforming tab character in column 2 of line 32
Warning: Nonconforming tab character in column 1 of line 33
Warning: Nonconforming tab character in column 1 of line 34
Warning: Nonconforming tab character in column 1 of line 35
Warning: Nonconforming tab character in column 3 of line 36
Warning: Nonconforming tab character in column 1 of line 37
Warning: Nonconforming tab character in column 1 of line 38
Warning: Nonconforming tab character in column 3 of line 39
Warning: Nonconforming tab character in column 1 of line 40
Warning: Nonconforming tab character in column 1 of line 41
Warning: Nonconforming tab character in column 1 of line 42
Warning: Nonconforming tab character in column 4 of line 43
Warning: Nonconforming tab character in column 1 of line 44
Warning: Nonconforming tab character in column 1 of line 45
Warning: Nonconforming tab character in column 1 of line 46
Warning: Nonconforming tab character in column 1 of line 47
Warning: Nonconforming tab character in column 1 of line 48
Warning: Nonconforming tab character in column 1 of line 50
Warning: Nonconforming tab character in column 1 of line 51
Warning: Nonconforming tab character in column 1 of line 52
Warning: Nonconforming tab character in column 1 of line 53
Warning: Nonconforming tab character in column 1 of line 54
Warning: Nonconforming tab character in column 1 of line 55
Warning: Nonconforming tab character in column 1 of line 56
Warning: Nonconforming tab character in column 1 of line 57
Warning: Nonconforming tab character in column 1 of line 58
Warning: Nonconforming tab character in column 1 of line 59
Warning: Nonconforming tab character in column 1 of line 60
Warning: Nonconforming tab character in column 1 of line 61
Warning: Nonconforming tab character in column 1 of line 62
Warning: Nonconforming tab character in column 1 of line 63
Warning: Nonconforming tab character in column 3 of line 64
Warning: Nonconforming tab character in column 1 of line 65
Warning: Nonconforming tab character in column 1 of line 66
Warning: Nonconforming tab character in column 3 of line 67
Warning: Nonconforming tab character in column 1 of line 68
Warning: Nonconforming tab character in column 1 of line 69
Warning: Nonconforming tab character in column 3 of line 71
Warning: Nonconforming tab character in column 1 of line 72
Warning: Nonconforming tab character in column 1 of line 73
Warning: Nonconforming tab character in column 3 of line 74
Warning: Nonconforming tab character in column 1 of line 75
Warning: Nonconforming tab character in column 1 of line 76
Warning: Nonconforming tab character in column 1 of line 77
Warning: Nonconforming tab character in column 1 of line 78
Warning: Nonconforming tab character in column 1 of line 79
Warning: Nonconforming tab character in column 3 of line 80
Warning: Nonconforming tab character in column 1 of line 81
Warning: Nonconforming tab character in column 1 of line 82
Warning: Nonconforming tab character in column 3 of line 83
Warning: Nonconforming tab character in column 1 of line 84
Warning: Nonconforming tab character in column 1 of line 85
Warning: Nonconforming tab character in column 1 of line 87
Warning: Nonconforming tab character in column 1 of line 88
Warning: Nonconforming tab character in column 1 of line 89
Warning: Nonconforming tab character in column 1 of line 90
Warning: Nonconforming tab character in column 3 of line 91
Warning: Nonconforming tab character in column 1 of line 92
Warning: Nonconforming tab character in column 1 of line 93
Warning: Nonconforming tab character in column 3 of line 94
Warning: Nonconforming tab character in column 1 of line 95
Warning: Nonconforming tab character in column 1 of line 96
dsmooth.f:62.20:

      do 10 i=1,n-1                                                     
                    1
Warning: Nonconforming tab character at (1)
dsmooth.f:70.7:

     &       diff(i-1)*diff(i+1) .lt. 0.) isplit(i)=1                   
       1
Warning: Nonconforming tab character at (1)
dsmooth.f: In function ‘amed3’:
dsmooth.f:50:0: warning: ‘__result_amed3’ may be used uninitialized in this function [-Wuninitialized]
gfortran   -fpic  -g -O2  -Wall -c idamax.f -o idamax.o
gcc -std=gnu99 -shared -L/usr/local/lib -o CNAnorm.so daxpy.o ddot.o dgbfa.o dgbsl.o dscal.o dsmooth.o idamax.o -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.13-bioc/meat/CNAnorm.Rcheck/CNAnorm/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CNAnorm)

name	user	system	elapsed
CNAnorm-class	0.024	0.004	0.028
DerivData-class	0.036	0.004	0.038
InData-class	0.008	0.000	0.009
Params-class	0.008	0.000	0.009
addDNACopy-methods	0.952	0.000	0.953
addSmooth-methods	0.588	0.000	0.591
chrsAndpos-methods	0.076	0.000	0.077
dataFrame2object	0.008	0.000	0.008
discreteNorm-methods	0.048	0.000	0.050
exportTable-method	0.064	0.000	0.063
gcNorm-methods	0.448	0.000	0.451
peakPloidy	20.101	0.024	20.177
plotGenome-methods	1.04	0.00	1.04
plotPeaks-methods	0.040	0.000	0.037
ratio-methods	0.460	0.000	0.459
suggValid-methods	0.016	0.000	0.013
validation-methods	0.008	0.004	0.011