I'm trying to install adegenet package using install_github(), but I get a few errors. I'm able to install the package if I build and install the package from console. For the latter output see below. I'm using 64-bit Windows 7. I wonder to what can we attribute the discrepancy between these two ways of installing a package?
> install_github("thibautjombart/adegenet/pkg")
Downloading github repo thibautjombart/adegenet@master
Installing adegenet
"C:/PROGRA~1/R/R-31~1.2/bin/x64/R" --vanilla CMD INSTALL \
"C:/Users/romunov/AppData/Local/Temp/RtmpSo6w8C/devtools15882f7c4022/thibautjombart-adegenet-8cca9e1/pkg" \
--library="C:/Users/romunov/Documents/R/win-library/3.1" --install-tests
* installing *source* package 'adegenet' ...
** libs
*** arch - i386
gcc -m32 -shared -s -static-libgcc -o adegenet.dll tmp.def GLfunctions.o adesub.o monmonier-utils.o sharedAll.o snpbin.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LC:/PROGRA~1/R/R-31~1.2/bin/i386 -lR
Cannot export AreaSign: symbol not found
Cannot export Assignpx: symbol not found
Cannot export Between: symbol not found
Cannot export CheckAllSeg: symbol not found
Cannot export Collinear: symbol not found
Cannot export DiagobgComp: symbol not found
Cannot export GLdotProd: symbol not found
Cannot export GLsumFreq: symbol not found
Cannot export GLsumInt: symbol not found
Cannot export NEARZERO: symbol not found
Cannot export Parallel: symbol not found
Cannot export SegSeg: symbol not found
Cannot export alea: symbol not found
Cannot export aleapermutmat: symbol not found
Cannot export aleapermutvec: symbol not found
Cannot export binIntToBytes: symbol not found
Cannot export byteToBinDouble: symbol not found
Cannot export byteToBinInt: symbol not found
Cannot export bytesToBinInt: symbol not found
Cannot export bytesToDouble: symbol not found
Cannot export bytesToInt: symbol not found
Cannot export dAbs: symbol not found
Cannot export dEqual: symbol not found
Cannot export dtodelta: symbol not found
Cannot export freeinttab: symbol not found
Cannot export freeintvec: symbol not found
Cannot export freetab: symbol not found
Cannot export freevec: symbol not found
Cannot export genlightTogenlightC: symbol not found
Cannot export getpermutation: symbol not found
Cannot export initvec: symbol not found
Cannot export makesnpbin: symbol not found
Cannot export matcentrage: symbol not found
Cannot export matmodifcm: symbol not found
Cannot export matmodifcn: symbol not found
Cannot export matmodifcp: symbol not found
Cannot export matmodifcs: symbol not found
Cannot export matmodiffc: symbol not found
Cannot export matpermut: symbol not found
Cannot export maxvec: symbol not found
Cannot export min_int: symbol not found
Cannot export nLoc: symbol not found
Cannot export nb_shared_all: symbol not found
Cannot export ploidy: symbol not found
Cannot export printsnpbin: symbol not found
Cannot export prodmatAAtB: symbol not found
Cannot export prodmatABC: symbol not found
Cannot export prodmatAtAB: symbol not found
Cannot export prodmatAtBC: symbol not found
Cannot export prodmatAtBrandomC: symbol not found
Cannot export sharedAll: symbol not found
Cannot export snpbin2freq: symbol not found
Cannot export snpbin2intvec: symbol not found
Cannot export snpbin_dotprod_freq: symbol not found
Cannot export snpbin_dotprod_int: symbol not found
Cannot export snpbin_isna: symbol not found
Cannot export sqrvec: symbol not found
Cannot export taballoc: symbol not found
Cannot export tabintalloc: symbol not found
Cannot export testRaw: symbol not found
Cannot export testSizePointer: symbol not found
Cannot export traceXtdLXq: symbol not found
Cannot export trild: symbol not found
Cannot export trildintswap: symbol not found
Cannot export trildswap: symbol not found
Cannot export trirap: symbol not found
Cannot export trirapideint: symbol not found
Cannot export trirapideintswap: symbol not found
Cannot export vecalloc: symbol not found
Cannot export vecintalloc: symbol not found
Cannot export vecpermut: symbol not found
c:/rtools/gcc-4.6.3/bin/../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/bin/ld.exe: i386:x86-64 architecture of input file `GLfunctions.o' is incompatible with i386 output
c:/rtools/gcc-4.6.3/bin/../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/bin/ld.exe: i386:x86-64 architecture of input file `adesub.o' is incompatible with i386 output
c:/rtools/gcc-4.6.3/bin/../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/bin/ld.exe: i386:x86-64 architecture of input file `monmonier-utils.o' is incompatible with i386 output
c:/rtools/gcc-4.6.3/bin/../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/bin/ld.exe: i386:x86-64 architecture of input file `sharedAll.o' is incompatible with i386 output
c:/rtools/gcc-4.6.3/bin/../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/bin/ld.exe: i386:x86-64 architecture of input file `snpbin.o' is incompatible with i386 output
GLfunctions.o: In function `GLsumInt':
/home/thibaut/dev/adegenet/pkg/src/GLfunctions.c:85: undefined reference to `calloc'
GLfunctions.o: In function `GLsumFreq':
/home/thibaut/dev/adegenet/pkg/src/GLfunctions.c:116: undefined reference to `calloc'
adesub.o: In function `tabintalloc':
/home/thibaut/dev/adegenet/pkg/src/adesub.c:58: undefined reference to `calloc'
/home/thibaut/dev/adegenet/pkg/src/adesub.c:63: undefined reference to `calloc'
/home/thibaut/dev/adegenet/pkg/src/adesub.c:66: undefined reference to `free'
adesub.o: In function `freeinttab':
/home/thibaut/dev/adegenet/pkg/src/adesub.c:92: undefined reference to `free'
adesub.o: In function `alea':
/home/thibaut/dev/adegenet/pkg/src/adesub.c:148: undefined reference to `rand'
adesub.o: In function `freetab':
/home/thibaut/dev/adegenet/pkg/src/adesub.c:450: undefined reference to `free'
adesub.o: In function `sqrvec':
/home/thibaut/dev/adegenet/pkg/src/adesub.c:950: undefined reference to `sqrt'
adesub.o: In function `taballoc':
/home/thibaut/dev/adegenet/pkg/src/adesub.c:962: undefined reference to `calloc'
/home/thibaut/dev/adegenet/pkg/src/adesub.c:964: undefined reference to `calloc'
adesub.o: In function `vecalloc':
/home/thibaut/dev/adegenet/pkg/src/adesub.c:1098: undefined reference to `calloc'
adesub.o: In function `matmodifcs':
/home/thibaut/dev/adegenet/pkg/src/adesub.c:663: undefined reference to `sqrt'
adesub.o: In function `matmodifcn':
/home/thibaut/dev/adegenet/pkg/src/adesub.c:611: undefined reference to `sqrt'
adesub.o: In function `DiagobgComp':
/home/thibaut/dev/adegenet/pkg/src/adesub.c:369: undefined reference to `sqrt'
/home/thibaut/dev/adegenet/pkg/src/adesub.c:245: undefined reference to `sqrt'
/home/thibaut/dev/adegenet/pkg/src/adesub.c:357: undefined reference to `sqrt'
adesub.o:/home/thibaut/dev/adegenet/pkg/src/adesub.c:339: more undefined references to `sqrt' follow
adesub.o: In function `vecintalloc':
/home/thibaut/dev/adegenet/pkg/src/adesub.c:1111: undefined reference to `calloc'
adesub.o: In function `getpermutation':
/home/thibaut/dev/adegenet/pkg/src/adesub.c:491: undefined reference to `clock'
/home/thibaut/dev/adegenet/pkg/src/adesub.c:493: undefined reference to `srand'
/home/thibaut/dev/adegenet/pkg/src/adesub.c:495: undefined reference to `rand'
/home/thibaut/dev/adegenet/pkg/src/adesub.c:491: undefined reference to `clock'
/home/thibaut/dev/adegenet/pkg/src/adesub.c:493: undefined reference to `srand'
adesub.o: In function `freeinttab':
/home/thibaut/dev/adegenet/pkg/src/adesub.c:95: undefined reference to `free'
adesub.o: In function `freeintvec':
/home/thibaut/dev/adegenet/pkg/src/adesub.c:437: undefined reference to `free'
adesub.o: In function `freetab':
/home/thibaut/dev/adegenet/pkg/src/adesub.c:452: undefined reference to `free'
adesub.o: In function `freevec':
/home/thibaut/dev/adegenet/pkg/src/adesub.c:460: undefined reference to `free'
snpbin.o: In function `byteToBinInt':
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:105: undefined reference to `pow'
snpbin.o: In function `byteToBinDouble':
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:128: undefined reference to `pow'
snpbin.o: In function `bytesToBinInt':
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:146: undefined reference to `calloc'
snpbin.o: In function `bytesToInt':
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:185: undefined reference to `calloc'
snpbin.o: In function `bytesToDouble':
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:213: undefined reference to `calloc'
snpbin.o: In function `binIntToBytes':
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:253: undefined reference to `pow'
snpbin.o: In function `snpbin2intvec':
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:315: undefined reference to `calloc'
snpbin.o: In function `snpbin2freq':
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:330: undefined reference to `calloc'
snpbin.o: In function `printsnpbin':
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:349: undefined reference to `calloc'
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:354: undefined reference to `Rprintf'
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:357: undefined reference to `Rprintf'
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:359: undefined reference to `Rprintf'
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:363: undefined reference to `Rprintf'
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:365: undefined reference to `Rprintf'
snpbin.o: In function `snpbin_dotprod_int':
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:399: undefined reference to `calloc'
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:400: undefined reference to `calloc'
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:429: undefined reference to `free'
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:430: undefined reference to `free'
snpbin.o: In function `snpbin_dotprod_freq':
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:446: undefined reference to `calloc'
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:447: undefined reference to `calloc'
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:476: undefined reference to `free'
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:477: undefined reference to `free'
snpbin.o: In function `genlightTogenlightC':
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:494: undefined reference to `calloc'
snpbin.o: In function `testSizePointer':
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:540: undefined reference to `calloc'
snpbin.o: In function `bytesToBinInt':
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:156: undefined reference to `free'
snpbin.o: In function `bytesToInt':
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:203: undefined reference to `free'
snpbin.o: In function `bytesToDouble':
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:230: undefined reference to `free'
snpbin.o: In function `snpbin2intvec':
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:318: undefined reference to `free'
snpbin.o: In function `snpbin2freq':
/home/thibaut/dev/adegenet/pkg/src/snpbin.c:338: undefined reference to `free'
snpbin.o:/home/thibaut/dev/adegenet/pkg/src/snpbin.c:369: more undefined references to `free' follow
collect2: ld returned 1 exit status
no DLL was created
ERROR: compilation failed for package 'adegenet'
* removing 'C:/Users/romunov/Documents/R/win-library/3.1/adegenet'
* restoring previous 'C:/Users/romunov/Documents/R/win-library/3.1/adegenet'
Show Traceback
Rerun with Debug
Error: Command failed (1)
This is the check log:
* using log directory 'D:/R/adegenet.Rcheck'
* using R version 3.1.2 (2014-10-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: CP1250
* checking for file 'adegenet/DESCRIPTION' ... OK
* this is package 'adegenet' version '1.4-3'
* 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'adegenet' can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.2Mb
sub-directories of 1Mb or more:
data 2.6Mb
files 1.6Mb
* checking package 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 ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 ... NOTE
HWE.test.genind : ftest: no visible global function definition for
'HWE.chisq'
HWE.test.genind : ftest: no visible global function definition for
'genotype'
alignment2genind: no visible binding for global variable 's2c'
chooseCN: no visible global function definition for 'tri2nb'
chooseCN: no visible global function definition for 'gabrielneigh'
chooseCN: no visible global function definition for 'graph2nb'
chooseCN: no visible global function definition for 'relativeneigh'
chooseCN: no visible global function definition for 'dnearneigh'
chooseCN: no visible global function definition for 'knearneigh'
chooseCN: no visible global function definition for 'knn2nb'
chooseCN: no visible global function definition for 'nb2listw'
chooseCN: no visible global function definition for 'mat2listw'
fasta2DNAbin: no visible global function definition for 'seg.sites'
fasta2genlight: no visible global function definition for 'mclapply'
fstat: no visible global function definition for 'varcomp.glob'
genind2genotype : f2: no visible global function definition for
'as.genotype'
genind2genotype: no visible global function definition for
'makeGenotypes'
glPca: no visible global function definition for 'mclapply'
gstat.randtest: no visible global function definition for
'g.stats.glob'
gstat.randtest : <anonymous>: no visible global function definition for
'g.stats.glob'
gstat.randtest : <anonymous>: no visible global function definition for
'samp.within'
gstat.randtest : <anonymous>: no visible global function definition for
'samp.between'
plot.spca: no visible global function definition for 'card'
read.PLINK: no visible global function definition for 'mclapply'
read.snp: no visible global function definition for 'mclapply'
snpposi.plot.DNAbin: no visible global function definition for
'seg.sites'
snpposi.test.DNAbin: no visible global function definition for
'seg.sites'
spca: no visible global function definition for 'mat2listw'
spca: no visible global function definition for 'nb2listw'
summary.spca: no visible global function definition for 'listw2mat'
summary.spca: no visible binding for global variable 'lag.listw'
* 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 ... WARNING
Note: significantly better compression could be obtained
by using R CMD build --resave-data
old_size new_size compress
H3N2.RData 108Kb 49Kb xz
dapcIllus.RData 84Kb 38Kb bzip2
eHGDP.RData 2.2Mb 1.1Mb bzip2
microbov.RData 57Kb 29Kb bzip2
rupica.RData 43Kb 31Kb xz
sim2pop.RData 10Kb 7Kb bzip2
spcaIllus.RData 29Kb 16Kb bzip2
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File 'adegenet/libs/i386/adegenet.dll':
Found 'rand', possibly from 'rand' (C)
Object: 'adesub.o'
Found 'srand', possibly from 'srand' (C)
Object: 'adesub.o'
File 'adegenet/libs/x64/adegenet.dll':
Found 'rand', possibly from 'rand' (C)
Object: 'adesub.o'
Found 'srand', possibly from 'srand' (C)
Object: 'adesub.o'
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the C RNG.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking PDF version of manual ... OK
* DONE
WARNING: There was 1 warning.
NOTE: There were 3 notes.
and the installation process
D:\R>R CMD INSTALL --build adegenet_1.4-3.tar.gz
* installing to library 'C:/Users/romunov/Documents/R/win-library/3.1'
* installing *source* package 'adegenet' ...
** libs
*** arch - i386
cygwin warning:
MS-DOS style path detected: C:/PROGRA~1/R/R-31~1.2/etc/i386/Makeconf
Preferred POSIX equivalent is: /cygdrive/c/PROGRA~1/R/R-31~1.2/etc/i386/Makeco
nf
CYGWIN environment variable option "nodosfilewarning" turns off this warning.
Consult the user's guide for more details about POSIX paths:
http://cygwin.com/cygwin-ug-net/using.html#using-pathnames
gcc -m32 -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG -DSUPPORT_OPENMP -I"d:/R
Compile/CRANpkg/extralibs64/local/include" -O2 -std=gnu99 -mtune=core2 -c G
Lfunctions.c -o GLfunctions.o
gcc -m32 -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG -DSUPPORT_OPENMP -I"d:/R
Compile/CRANpkg/extralibs64/local/include" -O2 -std=gnu99 -mtune=core2 -c a
desub.c -o adesub.o
gcc -m32 -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG -DSUPPORT_OPENMP -I"d:/R
Compile/CRANpkg/extralibs64/local/include" -O2 -std=gnu99 -mtune=core2 -c m
onmonier-utils.c -o monmonier-utils.o
gcc -m32 -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG -DSUPPORT_OPENMP -I"d:/R
Compile/CRANpkg/extralibs64/local/include" -O2 -std=gnu99 -mtune=core2 -c s
haredAll.c -o sharedAll.o
gcc -m32 -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG -DSUPPORT_OPENMP -I"d:/R
Compile/CRANpkg/extralibs64/local/include" -O2 -std=gnu99 -mtune=core2 -c s
npbin.c -o snpbin.o
gcc -m32 -shared -s -static-libgcc -o adegenet.dll tmp.def GLfunctions.o adesub.
o monmonier-utils.o sharedAll.o snpbin.o -Ld:/RCompile/CRANpkg/extralibs64/local
/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LC:/PROGRA~1/R/R-31~1.2/b
in/i386 -lR
installing to C:/Users/romunov/Documents/R/win-library/3.1/adegenet/libs/i386
*** arch - x64
cygwin warning:
MS-DOS style path detected: C:/PROGRA~1/R/R-31~1.2/etc/x64/Makeconf
Preferred POSIX equivalent is: /cygdrive/c/PROGRA~1/R/R-31~1.2/etc/x64/Makecon
f
CYGWIN environment variable option "nodosfilewarning" turns off this warning.
Consult the user's guide for more details about POSIX paths:
http://cygwin.com/cygwin-ug-net/using.html#using-pathnames
gcc -m64 -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG -DSUPPORT_OPENMP -I"d:/R
Compile/CRANpkg/extralibs64/local/include" -O2 -std=gnu99 -mtune=core2 -c G
Lfunctions.c -o GLfunctions.o
gcc -m64 -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG -DSUPPORT_OPENMP -I"d:/R
Compile/CRANpkg/extralibs64/local/include" -O2 -std=gnu99 -mtune=core2 -c a
desub.c -o adesub.o
gcc -m64 -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG -DSUPPORT_OPENMP -I"d:/R
Compile/CRANpkg/extralibs64/local/include" -O2 -std=gnu99 -mtune=core2 -c m
onmonier-utils.c -o monmonier-utils.o
gcc -m64 -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG -DSUPPORT_OPENMP -I"d:/R
Compile/CRANpkg/extralibs64/local/include" -O2 -std=gnu99 -mtune=core2 -c s
haredAll.c -o sharedAll.o
gcc -m64 -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG -DSUPPORT_OPENMP -I"d:/R
Compile/CRANpkg/extralibs64/local/include" -O2 -std=gnu99 -mtune=core2 -c s
npbin.c -o snpbin.o
gcc -m64 -shared -s -static-libgcc -o adegenet.dll tmp.def GLfunctions.o adesub.
o monmonier-utils.o sharedAll.o snpbin.o -Ld:/RCompile/CRANpkg/extralibs64/local
/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LC:/PROGRA~1/R/R-31~1.2/bi
n/x64 -lR
installing to C:/Users/romunov/Documents/R/win-library/3.1/adegenet/libs/x64
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'plot' from package 'graphics' in package 'adege
net'
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
*** arch - i386
*** arch - x64
* MD5 sums
packaged installation of 'adegenet' as adegenet_1.4-3.zip
* DONE (adegenet)