BioC 3.4: CHECK report for destiny on zin1

Package: destiny

Version: 1.99.11

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings destiny_1.99.11.tar.gz

StartedAt: 2016-09-20 05:33:40 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 05:35:46 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 126.0 seconds

RetCode: 0

Status:  OK

CheckDir: destiny.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings destiny_1.99.11.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/destiny.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 ‘destiny/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘destiny’ version ‘1.99.11’
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘destiny’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 ... NOTE
Warning: no function found corresponding to methods exports from ‘destiny’ for: ‘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 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 ... NOTE
S3 methods shown with full name in documentation object 'plot.DPT':
  ‘plot.DPT’

S3 methods shown with full name in documentation object 'plot.DiffusionMap':
  ‘plot.DiffusionMap’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
destiny 29.364  0.008  29.395
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' calls not declared from:
  ‘IRdisplay’ ‘IRkernel’ ‘base64enc’ ‘repr’ ‘xlsx’
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/destiny.Rcheck/00check.log’
for details.

* installing *source* package ‘destiny’ ...
** libs
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include"  -g -fpic  -g -O2 -c RcppExports.cpp -o RcppExports.o
In file included from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/Core:276:0,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/Dense:1,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigenForward.h:30,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigen.h:25,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/src/Core/Functors.h:973:28: warning: ‘template<class _Operation> class std::binder2nd’ is deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder2nd<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from /usr/include/c++/5/bits/locale_classes.h:40,
                 from /usr/include/c++/5/bits/ios_base.h:41,
                 from /usr/include/c++/5/ios:42,
                 from /usr/include/c++/5/ostream:38,
                 from /usr/include/c++/5/iterator:64,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigenForward.h:25,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigen.h:25,
                 from RcppExports.cpp:4:
/usr/include/c++/5/backward/binders.h:143:11: note: declared here
     class binder2nd
           ^
In file included from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/Core:276:0,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/Dense:1,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigenForward.h:30,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigen.h:25,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/src/Core/Functors.h:977:28: warning: ‘template<class _Operation> class std::binder1st’ is deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder1st<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from /usr/include/c++/5/bits/locale_classes.h:40,
                 from /usr/include/c++/5/bits/ios_base.h:41,
                 from /usr/include/c++/5/ios:42,
                 from /usr/include/c++/5/ostream:38,
                 from /usr/include/c++/5/iterator:64,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigenForward.h:25,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigen.h:25,
                 from RcppExports.cpp:4:
/usr/include/c++/5/backward/binders.h:108:11: note: declared here
     class binder1st
           ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include"  -g -fpic  -g -O2 -c censoring.cpp -o censoring.o
In file included from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/Core:276:0,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/Dense:1,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigenForward.h:30,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigen.h:25,
                 from censoring.cpp:7:
/home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/src/Core/Functors.h:973:28: warning: ‘template<class _Operation> class std::binder2nd’ is deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder2nd<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from /usr/include/c++/5/stdexcept:39,
                 from /usr/include/c++/5/array:38,
                 from /usr/include/c++/5/tuple:39,
                 from /usr/include/c++/5/unordered_map:41,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp/platform/compiler.h:153,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp/r/headers.h:48,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:29,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from censoring.cpp:6:
/usr/include/c++/5/backward/binders.h:143:11: note: declared here
     class binder2nd
           ^
In file included from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/Core:276:0,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/Dense:1,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigenForward.h:30,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigen.h:25,
                 from censoring.cpp:7:
/home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/src/Core/Functors.h:977:28: warning: ‘template<class _Operation> class std::binder1st’ is deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder1st<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from /usr/include/c++/5/stdexcept:39,
                 from /usr/include/c++/5/array:38,
                 from /usr/include/c++/5/tuple:39,
                 from /usr/include/c++/5/unordered_map:41,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp/platform/compiler.h:153,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp/r/headers.h:48,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:29,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from censoring.cpp:6:
/usr/include/c++/5/backward/binders.h:108:11: note: declared here
     class binder1st
           ^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include"  -g -fpic  -g -O2 -c no_censoring.cpp -o no_censoring.o
In file included from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/Core:276:0,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/Dense:1,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigenForward.h:30,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigen.h:25,
                 from no_censoring.cpp:5:
/home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/src/Core/Functors.h:973:28: warning: ‘template<class _Operation> class std::binder2nd’ is deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder2nd<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from /usr/include/c++/5/stdexcept:39,
                 from /usr/include/c++/5/array:38,
                 from /usr/include/c++/5/tuple:39,
                 from /usr/include/c++/5/unordered_map:41,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp/platform/compiler.h:153,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp/r/headers.h:48,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:29,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from no_censoring.cpp:4:
/usr/include/c++/5/backward/binders.h:143:11: note: declared here
     class binder2nd
           ^
In file included from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/Core:276:0,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/Dense:1,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigenForward.h:30,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigen.h:25,
                 from no_censoring.cpp:5:
/home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/src/Core/Functors.h:977:28: warning: ‘template<class _Operation> class std::binder1st’ is deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder1st<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from /usr/include/c++/5/stdexcept:39,
                 from /usr/include/c++/5/array:38,
                 from /usr/include/c++/5/tuple:39,
                 from /usr/include/c++/5/unordered_map:41,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp/platform/compiler.h:153,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp/r/headers.h:48,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:29,
                 from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from no_censoring.cpp:4:
/usr/include/c++/5/backward/binders.h:108:11: note: declared here
     class binder1st
           ^
g++ -std=c++11 -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o destiny.so RcppExports.o censoring.o no_censoring.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/destiny.Rcheck/destiny/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
Creating a generic function for ‘print’ from package ‘base’ in package ‘destiny’
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘destiny’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (destiny)

name	user	system	elapsed
DPT-methods	2.376	0.024	2.402
DPT	1.576	0.004	1.583
DiffusionMap-accessors	0.840	0.012	0.852
DiffusionMap-class	3.276	0.004	3.280
ExpressionSet-helpers	0.08	0.00	0.08
Sigmas-class	0.304	0.000	0.305
coercions	1.136	0.008	1.143
colorlegend	0.004	0.000	0.005
cube_helix	0.004	0.000	0.006
destiny	29.364	0.008	29.395
dm_predict	0.564	0.004	0.570
extractions	1.668	0.004	1.672
find_dm_k	0.004	0.000	0.003
find_sigmas	1.116	0.008	1.124
l_which	0.000	0.000	0.001
plot.DPT	1.596	0.004	1.599
plot.DiffusionMap	0.980	0.012	0.994
plot.Sigmas	0.456	0.004	0.458