Package: fmcsR

Version: 1.24.0

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:fmcsR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings fmcsR_1.24.0.tar.gz

StartedAt: 2019-04-13 02:20:04 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 02:22:31 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 146.8 seconds

RetCode: 0

Status:  OK

CheckDir: fmcsR.Rcheck

Warnings: 0

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:fmcsR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings fmcsR_1.24.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/fmcsR.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'fmcsR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'fmcsR' version '1.24.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'fmcsR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'methods' 'ChemmineR'
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
* 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 ... OK
** 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 ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to 'ChemmineR' which was already attached by Depends.
  Please remove these calls from your code.
Namespaces in Imports field not imported from:
  'BiocGenerics' 'RUnit' 'methods'
  All declared Imports should be used.
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.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
fmcs: no visible global function definition for 'as'
fmcs: no visible global function definition for 'new'
fmcsBatch: no visible global function definition for 'as'
fmcsBatch : score: no visible global function definition for 'as'
plotMCS: no visible global function definition for 'par'
coerce,list-MCS: no visible global function definition for 'new'
Undefined global functions or variables:
  as new par
Consider adding
  importFrom("graphics", "par")
  importFrom("methods", "as", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... NOTE
Package has both 'src/Makevars.in' and 'src/Makevars'.
Installation with --no-configure' is unlikely to work.  If you intended
'src/Makevars' to be used on Windows, rename it to 'src/Makevars.win'
otherwise remove it.  If 'configure' created 'src/Makevars', you need a
'cleanup' script.
* 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 'C:/Users/biocbuild/bbs-3.8-bioc/R/library/fmcsR/libs/i386/fmcsR.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 use Fortran I/O
nor system RNGs. 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
fmcsR-package 1.69   0.00    8.11
fmcsBatch     0.05   0.02    5.92
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
fmcsR-package 1.26   0.01    7.55
fmcsBatch     0.02   0.02    6.09
* 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: 5 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/fmcsR.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/fmcsR_1.24.0.tar.gz && rm -rf fmcsR.buildbin-libdir && mkdir fmcsR.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=fmcsR.buildbin-libdir fmcsR_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL fmcsR_1.24.0.zip && rm fmcsR_1.24.0.tar.gz fmcsR_1.24.0.zip
###
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100 78201  100 78201    0     0   815k      0 --:--:-- --:--:-- --:--:--  848k

install for i386

* installing *source* package 'fmcsR' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c MCS.cpp -o MCS.o
MCS.cpp: In member function 'void FMCS::MCS::calculate()':
MCS.cpp:108:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int i = 0; i < atomCountOne; ++i) {
                                   ^
MCS.cpp:116:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int i = 0; i < atomCountTwo; ++i) {
                                   ^
In file included from MCSCompound.h:15:0,
                 from MCS.h:12,
                 from MCS.cpp:3:
MCSList.h: In instantiation of 'bool FMCS::MCSList<T>::contains(const T&) const [with T = unsigned int]':
MCS.cpp:381:69:   required from here
MCSList.h:143:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int i = 0; i < length; ++i) {
                           ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c MCSCompound.cpp -o MCSCompound.o
In file included from MCSCompound.cpp:5:0:
MCSRingDetector.h: In constructor 'FMCS::MCSRingDetector::Ring::Ring(const FMCS::MCSRingDetector::Edge&, const FMCS::MCSCompound*)':
MCSRingDetector.h:86:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int i = 0; i < this->vertexPath.size(); ++i) {
                                   ^
MCSRingDetector.h: In member function 'int FMCS::MCSRingDetector::Ring::rightVertex(size_t) const':
MCSRingDetector.h:142:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 if (vertexIndex < vertexPath.size()-1) {
                                 ^
MCSCompound.cpp: In member function 'void FMCS::MCSCompound::read(const string&)':
MCSCompound.cpp:157:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int i = 0; i < bondCount; ++i) {
                           ^
MCSCompound.cpp: In member function 'std::string FMCS::MCSCompound::subgraph(const size_t*, size_t, const string&) const':
MCSCompound.cpp:194:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int i = 0; i < indexLength; ++i) {
                           ^
MCSCompound.cpp: In member function 'const FMCS::MCSCompound::Bond* FMCS::MCSCompound::getBond(size_t, size_t) const':
MCSCompound.cpp:467:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for(int i = 0; i < bondCount; ++i) {
                          ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c MCSMap.cpp -o MCSMap.o
In file included from MCSMap.h:8:0,
                 from MCSMap.cpp:3:
MCSList.h: In instantiation of 'bool FMCS::MCSList<T>::contains(const T&) const [with T = unsigned int]':
MCSMap.cpp:28:36:   required from here
MCSList.h:143:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int i = 0; i < length; ++i) {
                           ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c MCSRingDetector.cpp -o MCSRingDetector.o
In file included from MCSRingDetector.cpp:13:0:
MCSRingDetector.h: In constructor 'FMCS::MCSRingDetector::Ring::Ring(const FMCS::MCSRingDetector::Edge&, const FMCS::MCSCompound*)':
MCSRingDetector.h:86:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int i = 0; i < this->vertexPath.size(); ++i) {
                                   ^
MCSRingDetector.h: In member function 'int FMCS::MCSRingDetector::Ring::rightVertex(size_t) const':
MCSRingDetector.h:142:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 if (vertexIndex < vertexPath.size()-1) {
                                 ^
MCSRingDetector.cpp: In member function 'void FMCS::MCSRingDetector::sortVertexQueue()':
MCSRingDetector.cpp:93:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int i = 0; i < vertexQueue.size(); ++i) {
                           ^
MCSRingDetector.cpp:94:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (int j = 0; j < queueSize-1-i; ++j ) {
                               ^
MCSRingDetector.cpp: In member function 'void FMCS::MCSRingDetector::convert()':
MCSRingDetector.cpp:149:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (int j = 0; j < degree; ++j) {
                               ^
MCSRingDetector.cpp: In member function 'void FMCS::MCSRingDetector::detect()':
MCSRingDetector.cpp:175:13: warning: unused variable 'aromaticCount' [-Wunused-variable]
         int aromaticCount = 0;
             ^
MCSRingDetector.cpp: In member function 'bool FMCS::MCSRingDetector::Ring::isSp2Hybridized(size_t, int, bool&) const':
MCSRingDetector.cpp:194:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (level > vertexPath.size()) {
                   ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c fmcs_R_wrap.cpp -o fmcs_R_wrap.o
fmcs_R_wrap.cpp: In function 'void fmcs_R_wrap(const char**, const char**, int*, int*, int*, int*, int*, int*, int*, const char**, const char**, const char**, const char**, const char**)':
fmcs_R_wrap.cpp:74:45: warning: 'runningMode' may be used uninitialized in this function [-Wmaybe-uninitialized]
             matchType, runningMode, *timeout);
                                             ^
fmcs_R_wrap.cpp:74:45: warning: 'matchType' may be used uninitialized in this function [-Wmaybe-uninitialized]
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c util.cpp -o util.o
util.cpp: In function 'std::string getUpper(const string&)':
util.cpp:11:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i = 0; i < upper.length(); ++i) {
                       ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o fmcsR.dll tmp.def MCS.o MCSCompound.o MCSMap.o MCSRingDetector.o fmcs_R_wrap.o util.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/fmcsR.buildbin-libdir/fmcsR/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'fmcsR'
    finding HTML links ... done
    MCS-class                               html  
    fmcs                                    html  
    fmcsBatch                               html  
    fmcsR-package                           html  
    fmcstest                                html  
    mcs2sdfset                              html  
    plotMCS                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'fmcsR' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c MCS.cpp -o MCS.o
MCS.cpp: In member function 'void FMCS::MCS::calculate()':
MCS.cpp:108:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int i = 0; i < atomCountOne; ++i) {
                                   ^
MCS.cpp:116:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int i = 0; i < atomCountTwo; ++i) {
                                   ^
In file included from MCSCompound.h:15:0,
                 from MCS.h:12,
                 from MCS.cpp:3:
MCSList.h: In instantiation of 'bool FMCS::MCSList<T>::contains(const T&) const [with T = long long unsigned int]':
MCS.cpp:381:69:   required from here
MCSList.h:143:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int i = 0; i < length; ++i) {
                           ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c MCSCompound.cpp -o MCSCompound.o
In file included from MCSCompound.cpp:5:0:
MCSRingDetector.h: In constructor 'FMCS::MCSRingDetector::Ring::Ring(const FMCS::MCSRingDetector::Edge&, const FMCS::MCSCompound*)':
MCSRingDetector.h:86:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int i = 0; i < this->vertexPath.size(); ++i) {
                                   ^
MCSRingDetector.h: In member function 'int FMCS::MCSRingDetector::Ring::rightVertex(size_t) const':
MCSRingDetector.h:142:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 if (vertexIndex < vertexPath.size()-1) {
                                 ^
MCSCompound.cpp: In member function 'void FMCS::MCSCompound::read(const string&)':
MCSCompound.cpp:157:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int i = 0; i < bondCount; ++i) {
                           ^
MCSCompound.cpp: In member function 'std::string FMCS::MCSCompound::subgraph(const size_t*, size_t, const string&) const':
MCSCompound.cpp:194:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int i = 0; i < indexLength; ++i) {
                           ^
MCSCompound.cpp: In member function 'const FMCS::MCSCompound::Bond* FMCS::MCSCompound::getBond(size_t, size_t) const':
MCSCompound.cpp:467:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for(int i = 0; i < bondCount; ++i) {
                          ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c MCSMap.cpp -o MCSMap.o
In file included from MCSMap.h:8:0,
                 from MCSMap.cpp:3:
MCSList.h: In instantiation of 'bool FMCS::MCSList<T>::contains(const T&) const [with T = long long unsigned int]':
MCSMap.cpp:28:36:   required from here
MCSList.h:143:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int i = 0; i < length; ++i) {
                           ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c MCSRingDetector.cpp -o MCSRingDetector.o
In file included from MCSRingDetector.cpp:13:0:
MCSRingDetector.h: In constructor 'FMCS::MCSRingDetector::Ring::Ring(const FMCS::MCSRingDetector::Edge&, const FMCS::MCSCompound*)':
MCSRingDetector.h:86:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int i = 0; i < this->vertexPath.size(); ++i) {
                                   ^
MCSRingDetector.h: In member function 'int FMCS::MCSRingDetector::Ring::rightVertex(size_t) const':
MCSRingDetector.h:142:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 if (vertexIndex < vertexPath.size()-1) {
                                 ^
MCSRingDetector.cpp: In member function 'void FMCS::MCSRingDetector::sortVertexQueue()':
MCSRingDetector.cpp:93:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int i = 0; i < vertexQueue.size(); ++i) {
                           ^
MCSRingDetector.cpp:94:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (int j = 0; j < queueSize-1-i; ++j ) {
                               ^
MCSRingDetector.cpp: In member function 'void FMCS::MCSRingDetector::convert()':
MCSRingDetector.cpp:149:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (int j = 0; j < degree; ++j) {
                               ^
MCSRingDetector.cpp: In member function 'void FMCS::MCSRingDetector::detect()':
MCSRingDetector.cpp:175:13: warning: unused variable 'aromaticCount' [-Wunused-variable]
         int aromaticCount = 0;
             ^
MCSRingDetector.cpp: In member function 'bool FMCS::MCSRingDetector::Ring::isSp2Hybridized(size_t, int, bool&) const':
MCSRingDetector.cpp:194:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (level > vertexPath.size()) {
                   ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c fmcs_R_wrap.cpp -o fmcs_R_wrap.o
fmcs_R_wrap.cpp: In function 'void fmcs_R_wrap(const char**, const char**, int*, int*, int*, int*, int*, int*, int*, const char**, const char**, const char**, const char**, const char**)':
fmcs_R_wrap.cpp:74:45: warning: 'runningMode' may be used uninitialized in this function [-Wmaybe-uninitialized]
             matchType, runningMode, *timeout);
                                             ^
fmcs_R_wrap.cpp:74:45: warning: 'matchType' may be used uninitialized in this function [-Wmaybe-uninitialized]
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c util.cpp -o util.o
util.cpp: In function 'std::string getUpper(const string&)':
util.cpp:11:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i = 0; i < upper.length(); ++i) {
                       ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o fmcsR.dll tmp.def MCS.o MCSCompound.o MCSMap.o MCSRingDetector.o fmcs_R_wrap.o util.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/fmcsR.buildbin-libdir/fmcsR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'fmcsR' as fmcsR_1.24.0.zip
* DONE (fmcsR)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'fmcsR' successfully unpacked and MD5 sums checked
In R CMD INSTALL