BioC 3.4: CHECK report for chopsticks on zin1

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings chopsticks_1.37.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/chopsticks.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘chopsticks/DESCRIPTION’ ... OK
* this is package ‘chopsticks’ version ‘1.37.0’
* 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 ‘chopsticks’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
Warning: no function found corresponding to methods exports from ‘chopsticks’ for: ‘cbind2’, ‘coerce’, ‘initialize’, ‘rbind2’, ‘show’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘methods:::bind_activation’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
NB: .Last.lib will not be used unless it is exported
File ‘chopsticks/R/zzz.R’:
  .Last.lib has wrong argument list ‘libname, package’

Package detach functions should have one argument with name starting
  with ‘lib’.
Package detach functions should not call ‘library.dynam.unload’.
See section ‘Good practice’ in '?.Last.lib'.

qq.chisq : shade: no visible global function definition for ‘polygon’
qq.chisq: no visible global function definition for ‘qchisq’
qq.chisq: no visible global function definition for ‘qbeta’
qq.chisq: no visible global function definition for ‘plot’
qq.chisq: no visible global function definition for ‘pchisq’
qq.chisq: no visible global function definition for ‘points’
qq.chisq: no visible global function definition for ‘abline’
qq.chisq: no visible global function definition for ‘legend’
read.HapMap.data: no visible global function definition for
  ‘download.file’
read.HapMap.data: no visible global function definition for
  ‘flush.console’
read.pedfile.info: no visible global function definition for
  ‘read.table’
read.pedfile.map: no visible global function definition for
  ‘read.table’
read.snps.long.old: no visible global function definition for ‘new’
read.snps.pedfile: no visible global function definition for
  ‘download.file’
single.snp.tests: no visible global function definition for ‘is’
snp.lhs.tests: no visible global function definition for ‘is’
snp.lhs.tests: no visible global function definition for ‘terms’
snp.lhs.tests: no visible global function definition for ‘model.matrix’
snp.rhs.tests: no visible global function definition for ‘terms’
snp.rhs.tests: no visible global function definition for ‘is’
snp.rhs.tests: no visible global function definition for
  ‘model.response’
snp.rhs.tests: no visible global function definition for ‘model.matrix’
snp.rhs.tests: no visible global function definition for
  ‘model.weights’
snp.rhs.tests: no visible global function definition for ‘model.offset’
write.snp.matrix: no visible global function definition for ‘is’
[,X.snp.matrix-ANY-ANY-ANY: no visible global function definition for
  ‘new’
[<-,X.snp.matrix-ANY-ANY-X.snp.matrix: no visible global function
  definition for ‘slot’
[<-,X.snp.matrix-ANY-ANY-X.snp.matrix: no visible global function
  definition for ‘slot<-’
coerce,X.snp-genotype: no visible global function definition for
  ‘callNextMethod’
coerce,matrix-snp.matrix: no visible global function definition for
  ‘new’
coerce,snp-genotype: no visible global function definition for ‘as’
coerce,snp.matrix-X.snp.matrix: no visible global function definition
  for ‘new’
initialize,X.snp.matrix: no visible global function definition for
  ‘callNextMethod’
initialize,snp.matrix: no visible global function definition for
  ‘callNextMethod’
show,X.snp: no visible global function definition for ‘as’
show,snp: no visible global function definition for ‘as’
Undefined global functions or variables:
  abline as callNextMethod download.file flush.console is legend
  model.matrix model.offset model.response model.weights new pchisq
  plot points polygon qbeta qchisq read.table slot slot<- terms
Consider adding
  importFrom("graphics", "abline", "legend", "plot", "points", "polygon")
  importFrom("methods", "as", "callNextMethod", "is", "new", "slot",
             "slot<-")
  importFrom("stats", "model.matrix", "model.offset", "model.response",
             "model.weights", "pchisq", "qbeta", "qchisq", "terms")
  importFrom("utils", "download.file", "flush.console", "read.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
prepare_Rd: ibs.stats.Rd:28: Dropping empty section \references
prepare_Rd: ibs.stats.Rd:49: Dropping empty section \seealso
prepare_Rd: read.pedfile.info.Rd:31-32: Dropping empty section \examples
prepare_Rd: read.pedfile.map.Rd:31-32: Dropping empty section \examples
prepare_Rd: read.snps.chiamo.Rd:37-38: Dropping empty section \note
prepare_Rd: read.wtccc.signals.Rd:58: Dropping empty section \seealso
prepare_Rd: wtccc.sample.list.Rd:36-37: Dropping empty section \note
prepare_Rd: wtccc.sample.list.Rd:39-40: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'X.snp.matrix,ANY,ANY,ANY'
  generic '[' and siglist 'snp.matrix,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 compiled code ... NOTE
File ‘chopsticks/libs/chopsticks.so’:
  Found non-API call to R: ‘R_data_class’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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
* DONE

Status: 1 WARNING, 7 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/chopsticks.Rcheck/00check.log’
for details.

* installing *source* package ‘chopsticks’ ...
** libs
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c adler32.c -o adler32.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c bind.c -o bind.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c compress.c -o compress.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c crc32.c -o crc32.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c deflate.c -o deflate.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c force_hom.c -o force_hom.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c glm_test.c -o glm_test.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c glm_test_R.c -o glm_test_R.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c gzio.c -o gzio.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c hash_index.c -o hash_index.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c ibs.c -o ibs.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c in.c -o in.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c infback.c -o infback.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c inffast.c -o inffast.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c inflate.c -o inflate.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c inftrees.c -o inftrees.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c input.c -o input.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c inputNew.c -o inputNew.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c input_unsorted.c -o input_unsorted.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c ld_graphic_eps.c -o ld_graphic_eps.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c ld_with.c -o ld_with.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c mla.c -o mla.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c outdata.c -o outdata.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c pairwise_linkage.c -o pairwise_linkage.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c read_chiamo.c -o read_chiamo.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c read_hapmap.c -o read_hapmap.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c read_pedfile.c -o read_pedfile.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c read_signals.c -o read_signals.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c readped.c -o readped.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c sdfpw.c -o sdfpw.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c single_snp_tests.c -o single_snp_tests.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c snp_summary.c -o snp_summary.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c snpmpy.c -o snpmpy.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c solve_cubic.c -o solve_cubic.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c solve_quadratic.c -o solve_quadratic.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c structure.c -o structure.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c trees.c -o trees.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c uncompr.c -o uncompr.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c zutil.c -o zutil.o
gcc -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o chopsticks.so adler32.o bind.o compress.o crc32.o deflate.o force_hom.o glm_test.o glm_test_R.o gzio.o hash_index.o ibs.o in.o infback.o inffast.o inflate.o inftrees.o input.o inputNew.o input_unsorted.o ld_graphic_eps.o ld_with.o mla.o outdata.o pairwise_linkage.o read_chiamo.o read_hapmap.o read_pedfile.o read_signals.o readped.o sdfpw.o single_snp_tests.o snp_summary.o snpmpy.o solve_cubic.o solve_quadratic.o structure.o trees.o uncompr.o zutil.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/chopsticks.Rcheck/chopsticks/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 (chopsticks)

name	user	system	elapsed
X.snp-class	0.192	0.000	0.192
X.snp.matrix-class	0.164	0.004	0.169
epsout.ld.snp	0.160	0.000	0.157
for.exercise	0.684	0.008	0.695
ibs.stats	0.172	0.000	0.175
ibsCount	0.232	0.000	0.231
ibsDist	0.172	0.000	0.171
ld.snp	0.152	0.000	0.149
ld.with	0.092	0.000	0.091
pair.result.ld.snp	0.076	0.000	0.077
plot.snp.dprime	0.240	0.000	0.238
qq.chisq	0	0	0
read.HapMap.data	0.004	0.000	0.001
read.snps.chiamo	0	0	0
read.wtccc.signals	0.000	0.000	0.001
row.summary	0.092	0.000	0.092
single.snp.tests	0.080	0.004	0.085
snp-class	0.000	0.000	0.001
snp.cbind	0.16	0.00	0.16
snp.cor	0.600	0.000	0.601
snp.dprime-class	0.080	0.004	0.082
snp.lhs.tests	0.100	0.000	0.098
snp.matrix-class	0.200	0.012	0.210
snp.pre	0.096	0.000	0.095
snp.rhs.tests	0.08	0.00	0.08
testdata	0.116	0.000	0.115
xxt	0.540	0.000	0.541

BioC 3.4: CHECK report for chopsticks on zin1

Summary

Command output