chopsticks 1.40.0
Hin-Tak Leung
| Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) | | URL: https://git.bioconductor.org/packages/chopsticks | | Branch: RELEASE_3_5 | | Last Commit: d9d5e6a | | Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | WARNINGS | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | [ WARNINGS ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings chopsticks_1.40.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/chopsticks.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘chopsticks/DESCRIPTION’ ... OK
* this is package ‘chopsticks’ version ‘1.40.0’
* 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 5.5Mb
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 in methods:::bind_activation(TRUE) :
methods:::bind_activation(TRUE) is deprecated;
you should rather provide methods for cbind2() / rbind2()
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
‘/Users/biocbuild/bbs-3.5-bioc/meat/chopsticks.Rcheck/00check.log’
for details.
* installing *source* package ‘chopsticks’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c adler32.c -o adler32.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c bind.c -o bind.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c compress.c -o compress.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c crc32.c -o crc32.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c deflate.c -o deflate.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c force_hom.c -o force_hom.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c glm_test.c -o glm_test.o
glm_test.c:155:14: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
(iter && (abs(wss-wss_last)/wss_last < conv));
^
glm_test.c:155:14: note: use function 'fabs' instead
(iter && (abs(wss-wss_last)/wss_last < conv));
^˜˜
fabs
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c glm_test_R.c -o glm_test_R.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c gzio.c -o gzio.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c hash_index.c -o hash_index.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c ibs.c -o ibs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c in.c -o in.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c infback.c -o infback.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c inffast.c -o inffast.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c inflate.c -o inflate.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c inftrees.c -o inftrees.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c input.c -o input.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c inputNew.c -o inputNew.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c input_unsorted.c -o input_unsorted.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c ld_graphic_eps.c -o ld_graphic_eps.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c ld_with.c -o ld_with.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c mla.c -o mla.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c outdata.c -o outdata.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c pairwise_linkage.c -o pairwise_linkage.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c read_chiamo.c -o read_chiamo.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c read_hapmap.c -o read_hapmap.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c read_pedfile.c -o read_pedfile.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c read_signals.c -o read_signals.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c readped.c -o readped.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c sdfpw.c -o sdfpw.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c single_snp_tests.c -o single_snp_tests.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c snp_summary.c -o snp_summary.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c snpmpy.c -o snpmpy.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c solve_cubic.c -o solve_cubic.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c solve_quadratic.c -o solve_quadratic.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c structure.c -o structure.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c trees.c -o trees.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c uncompr.c -o uncompr.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c zutil.c -o zutil.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-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
Warning in methods:::bind_activation(TRUE) :
methods:::bind_activation(TRUE) is deprecated;
you should rather provide methods for cbind2() / rbind2()
* DONE (chopsticks)