BioC 3.4: CHECK report for destiny on moscato1

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### Running command:
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###   rm -rf destiny.buildbin-libdir destiny.Rcheck && mkdir destiny.buildbin-libdir destiny.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=destiny.buildbin-libdir destiny_1.99.0.tar.gz >destiny.Rcheck\00install.out 2>&1 && cp destiny.Rcheck\00install.out destiny-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=destiny.buildbin-libdir --install="check:destiny-install.out" --force-multiarch --no-vignettes --timings destiny_1.99.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/destiny.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'destiny/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'destiny' version '1.99.0'
* 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 whether package 'destiny' can be installed ... WARNING
Found the following significant warnings:
  no_censoring.cpp:16:52: warning: operation on 'v1sqr_sum' may be undefined [-Wsequence-point]
See 'D:/biocbld/bbs-3.4-bioc/meat/destiny.Rcheck/00install.out' for details.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... WARNING
S4 class codoc mismatches from documentation object 'DiffusionMap class':
Slots for class 'DiffusionMap'
  Code: censor_range censor_val d d_norm data_env density_norm distance
        eigenvalues eigenvec0 eigenvectors k missing_range n_local
        sigmas transitions vars
  Docs: censor_range censor_val d d_norm data_env density_norm distance
        eigenvalues eigenvec0 eigenvectors k missing_range sigmas
        transitions vars

* checking Rd \usage sections ... NOTE
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 ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbld/bbs-3.4-bioc/meat/destiny.buildbin-libdir/destiny/libs/i386/destiny.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'destiny-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ExpressionSet helpers
> ### Title: Convert object to ExpressionSet or read it from a file
> ### Aliases: 'ExpressionSet helpers' as.ExpressionSet
> ###   as.ExpressionSet,data.frame-method as.ExpressionSet-method
> ###   read.ExpressionSet
> 
> ### ** Examples
> 
> df <- data.frame(Time  = seq_len(3), #integer column
+                  Actb  = c(0.05, 0.3, 0.8),
+                  Gapdh = c(0.2, 0.03, 0.1))
> set <- as.ExpressionSet(df)
> rownames(exprs(set)) == c('Actb', 'Gapdh')
Error in rownames(exprs(set)) : could not find function "exprs"
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'destiny-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ExpressionSet helpers
> ### Title: Convert object to ExpressionSet or read it from a file
> ### Aliases: 'ExpressionSet helpers' as.ExpressionSet
> ###   as.ExpressionSet,data.frame-method as.ExpressionSet-method
> ###   read.ExpressionSet
> 
> ### ** Examples
> 
> df <- data.frame(Time  = seq_len(3), #integer column
+                  Actb  = c(0.05, 0.3, 0.8),
+                  Gapdh = c(0.2, 0.03, 0.1))
> set <- as.ExpressionSet(df)
> rownames(exprs(set)) == c('Actb', 'Gapdh')
Error in rownames(exprs(set)) : could not find function "exprs"
Execution halted
* 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: 2 ERRORs, 2 WARNINGs, 5 NOTEs
See
  'D:/biocbld/bbs-3.4-bioc/meat/destiny.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'destiny' ...
** libs
C:/Rtools/mingw_32/bin/g++  -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppEigen/include" -I"c:/local323/include"  -g   -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppEigen/include" -I"c:/local323/include"  -g   -O2 -Wall  -mtune=core2 -c censoring.cpp -o censoring.o
C:/Rtools/mingw_32/bin/g++  -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppEigen/include" -I"c:/local323/include"  -g   -O2 -Wall  -mtune=core2 -c no_censoring.cpp -o no_censoring.o
no_censoring.cpp: In function 'double cor(Rcpp::NumericVector, Rcpp::NumericVector)':
no_censoring.cpp:16:52: warning: operation on 'v1sqr_sum' may be undefined [-Wsequence-point]
  v1sum = v2sum = v12sum = v1sqr_sum = v1sqr_sum = 0;
                                                    ^
no_censoring.cpp:27:54: warning: 'v2sqr_sum' may be used uninitialized in this function [-Wmaybe-uninitialized]
  const double deno = (n*v1sqr_sum - v1sum*v1sum) * (n*v2sqr_sum - v2sum*v2sum);
                                                      ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o destiny.dll tmp.def RcppExports.o censoring.o no_censoring.o -Lc:/local323/lib/i386 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/destiny.buildbin-libdir/destiny/libs/i386
** 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

install for x64

* installing *source* package 'destiny' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppEigen/include" -I"c:/local323/include"  -g   -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppEigen/include" -I"c:/local323/include"  -g   -O2 -Wall  -mtune=core2 -c censoring.cpp -o censoring.o
censoring.cpp: In function 'Rcpp::NumericMatrix predict_censoring_impl(Rcpp::NumericMatrix, Rcpp::NumericMatrix, double, Rcpp::NumericVector, Rcpp::NumericVector, double)':
censoring.cpp:72:17: warning: 'm1' may be used uninitialized in this function [-Wmaybe-uninitialized]
     / sqrt(m1-m0);
                 ^
censoring.cpp:55:15: note: 'm1' was declared here
    double m0, m1;
               ^
censoring.cpp:71:22: warning: 'm0' may be used uninitialized in this function [-Wmaybe-uninitialized]
     * ( std::erfc((m0-v) / sigma) - std::erfc((m1-v) / sigma) )
                      ^
censoring.cpp:55:11: note: 'm0' was declared here
    double m0, m1;
           ^
censoring.cpp:66:33: warning: 'use_d' may be used uninitialized in this function [-Wmaybe-uninitialized]
    const double v = use_d ? d : c;
                                 ^
censoring.cpp:18:7: note: 'use_d' was declared here
  bool use_d;
       ^
censoring.cpp: In function 'Eigen::SparseMatrix<double, 0, int> censoring_impl(Rcpp::NumericMatrix, SEXP, SEXP, SEXP, double, SEXP, Rcpp::Function)':
censoring.cpp:72:17: warning: 'm1' may be used uninitialized in this function [-Wmaybe-uninitialized]
     / sqrt(m1-m0);
                 ^
censoring.cpp:55:15: note: 'm1' was declared here
    double m0, m1;
               ^
censoring.cpp:71:22: warning: 'm0' may be used uninitialized in this function [-Wmaybe-uninitialized]
     * ( std::erfc((m0-v) / sigma) - std::erfc((m1-v) / sigma) )
                      ^
censoring.cpp:55:11: note: 'm0' was declared here
    double m0, m1;
           ^
censoring.cpp:66:33: warning: 'use_d' may be used uninitialized in this function [-Wmaybe-uninitialized]
    const double v = use_d ? d : c;
                                 ^
censoring.cpp:18:7: note: 'use_d' was declared here
  bool use_d;
       ^
C:/Rtools/mingw_64/bin/g++  -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppEigen/include" -I"c:/local323/include"  -g   -O2 -Wall  -mtune=core2 -c no_censoring.cpp -o no_censoring.o
no_censoring.cpp: In function 'double cor(Rcpp::NumericVector, Rcpp::NumericVector)':
no_censoring.cpp:16:52: warning: operation on 'v1sqr_sum' may be undefined [-Wsequence-point]
  v1sum = v2sum = v12sum = v1sqr_sum = v1sqr_sum = 0;
                                                    ^
no_censoring.cpp:27:54: warning: 'v2sqr_sum' may be used uninitialized in this function [-Wmaybe-uninitialized]
  const double deno = (n*v1sqr_sum - v1sum*v1sum) * (n*v2sqr_sum - v2sum*v2sum);
                                                      ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o destiny.dll tmp.def RcppExports.o censoring.o no_censoring.o -Lc:/local323/lib/x64 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/destiny.buildbin-libdir/destiny/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'destiny' as destiny_1.99.0.zip
* DONE (destiny)

name	user	system	elapsed
DiffusionMap-class	6.68	0.14	6.82
DiffusionMap-coercions	1.08	0.03	1.11
DiffusionMap-methods	1.07	0.06	1.13

name	user	system	elapsed
DiffusionMap-class	4.16	0.14	4.30
DiffusionMap-coercions	0.71	0.05	0.75
DiffusionMap-methods	1.09	0.09	1.19

BioC 3.4: CHECK report for destiny on moscato1

Summary

Command output