Package: ArrayExpressHTS

Version: 1.33.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ArrayExpressHTS

StartedAt: 2019-04-08 20:04:08 -0400 (Mon, 08 Apr 2019)

EndedAt: 2019-04-08 20:04:10 -0400 (Mon, 08 Apr 2019)

EllapsedTime: 2.0 seconds

RetCode: 1

Status:  ERROR

PackageFile: None

PackageFileSize: NA

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ArrayExpressHTS
###
##############################################################################
##############################################################################


* checking for file ‘ArrayExpressHTS/DESCRIPTION’ ... OK
* preparing ‘ArrayExpressHTS’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
      -----------------------------------
* installing *source* package ‘ArrayExpressHTS’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rsamtools/include" -I/usr/local/include  -fPIC  -Wall -g -O2  -c addXS.c -o addXS.o
addXS.c:42:5: warning: implicit declaration of function 'Rprintf' is invalid in C99 [-Wimplicit-function-declaration]
    Rprintf("What?\n");
    ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rsamtools/include" -I/usr/local/include  -fPIC  -Wall -g -O2  -c fltbam.c -o fltbam.o
fltbam.c:2:10: fatal error: 'samtools/sam.h' file not found
#include "samtools/sam.h"
         ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
1 error generated.
make: *** [fltbam.o] Error 1
ERROR: compilation failed for package ‘ArrayExpressHTS’
* removing ‘/private/tmp/RtmpaorUXN/Rinst725a34ca21d8/ArrayExpressHTS’
      -----------------------------------
ERROR: package installation failed