> install.packages(dir('.', pattern=".tar.gz$"), repos=NULL, type="source") Installing packages into ‘/home/asif/R/i686-pc-linux-gnu-library/3.1’ (as ‘lib’ is unspecified) ERROR: dependencies ‘BiocGenerics’, ‘Biobase’, ‘GenomeInfoDb’, ‘DBI’, ‘RSQLite’, ‘IRanges’ are not available for package ‘AnnotationDbi’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/AnnotationDbi’ * installing *source* package ‘base64enc’ ... ** package ‘base64enc’ successfully unpacked and MD5 sums checked ** libs sh: 1: gmake: not found ERROR: compilation failed for package ‘base64enc’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/base64enc’ ERROR: dependencies ‘BBmisc’, ‘digest’, ‘DBI’, ‘RSQLite’, ‘sendmailR’, ‘brew’, ‘plyr’, ‘stringr’, ‘fail’ are not available for package ‘BatchJobs’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/BatchJobs’ * installing *source* package ‘BBmisc’ ... ** package ‘BBmisc’ successfully unpacked and MD5 sums checked ** libs sh: 1: gmake: not found ERROR: compilation failed for package ‘BBmisc’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/BBmisc’ ERROR: dependency ‘BiocGenerics’ is not available for package ‘Biobase’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/Biobase’ * installing *source* package ‘BiocGenerics’ ... ** R ** inst ** preparing package for lazy loading Creating a new generic function for ‘append’ in package ‘BiocGenerics’ Creating a new generic function for ‘as.data.frame’ in package ‘BiocGenerics’ Creating a new generic function for ‘as.vector’ in package ‘BiocGenerics’ Creating a new generic function for ‘cbind’ in package ‘BiocGenerics’ Creating a new generic function for ‘rbind’ in package ‘BiocGenerics’ Creating a new generic function for ‘do.call’ in package ‘BiocGenerics’ Creating a new generic function for ‘duplicated’ in package ‘BiocGenerics’ Creating a new generic function for ‘anyDuplicated’ in package ‘BiocGenerics’ Creating a new generic function for ‘eval’ in package ‘BiocGenerics’ Creating a new generic function for ‘pmax’ in package ‘BiocGenerics’ Creating a new generic function for ‘pmin’ in package ‘BiocGenerics’ Creating a new generic function for ‘pmax.int’ in package ‘BiocGenerics’ Creating a new generic function for ‘pmin.int’ in package ‘BiocGenerics’ Creating a new generic function for ‘Reduce’ in package ‘BiocGenerics’ Creating a new generic function for ‘Filter’ in package ‘BiocGenerics’ Creating a new generic function for ‘Find’ in package ‘BiocGenerics’ Creating a new generic function for ‘Map’ in package ‘BiocGenerics’ Creating a new generic function for ‘Position’ in package ‘BiocGenerics’ Creating a new generic function for ‘get’ in package ‘BiocGenerics’ Creating a new generic function for ‘mget’ in package ‘BiocGenerics’ Creating a new generic function for ‘is.unsorted’ in package ‘BiocGenerics’ Creating a new generic function for ‘lapply’ in package ‘BiocGenerics’ Creating a new generic function for ‘sapply’ in package ‘BiocGenerics’ Creating a new generic function for ‘mapply’ in package ‘BiocGenerics’ Creating a new generic function for ‘match’ in package ‘BiocGenerics’ Creating a new generic function for ‘order’ in package ‘BiocGenerics’ Creating a new generic function for ‘paste’ in package ‘BiocGenerics’ Creating a new generic function for ‘rank’ in package ‘BiocGenerics’ Creating a new generic function for ‘rep.int’ in package ‘BiocGenerics’ Creating a new generic function for ‘rownames’ in package ‘BiocGenerics’ Creating a new generic function for ‘colnames’ in package ‘BiocGenerics’ Creating a new generic function for ‘union’ in package ‘BiocGenerics’ Creating a new generic function for ‘intersect’ in package ‘BiocGenerics’ Creating a new generic function for ‘setdiff’ in package ‘BiocGenerics’ Creating a new generic function for ‘sort’ in package ‘BiocGenerics’ Creating a new generic function for ‘table’ in package ‘BiocGenerics’ Creating a new generic function for ‘tapply’ in package ‘BiocGenerics’ Creating a new generic function for ‘unique’ in package ‘BiocGenerics’ Creating a new generic function for ‘unlist’ in package ‘BiocGenerics’ Creating a new generic function for ‘xtabs’ in package ‘BiocGenerics’ Creating a new generic function for ‘clusterCall’ in package ‘BiocGenerics’ Creating a new generic function for ‘clusterApply’ in package ‘BiocGenerics’ Creating a new generic function for ‘clusterApplyLB’ in package ‘BiocGenerics’ Creating a new generic function for ‘clusterEvalQ’ in package ‘BiocGenerics’ Warning in getPackageName(environment(fdef)) : Created a package name, ‘2014-03-31 11:43:22’, when none found Creating a new generic function for ‘clusterExport’ in package ‘BiocGenerics’ Creating a new generic function for ‘clusterMap’ in package ‘BiocGenerics’ Creating a new generic function for ‘parLapply’ in package ‘BiocGenerics’ Creating a new generic function for ‘parSapply’ in package ‘BiocGenerics’ Creating a new generic function for ‘parApply’ in package ‘BiocGenerics’ Creating a new generic function for ‘parRapply’ in package ‘BiocGenerics’ Creating a new generic function for ‘parCapply’ in package ‘BiocGenerics’ Creating a new generic function for ‘parLapplyLB’ in package ‘BiocGenerics’ Creating a new generic function for ‘parSapplyLB’ in package ‘BiocGenerics’ ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (BiocGenerics) ERROR: dependencies ‘foreach’, ‘BatchJobs’, ‘BBmisc’ are not available for package ‘BiocParallel’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/BiocParallel’ ERROR: dependencies ‘XML’, ‘RCurl’, ‘AnnotationDbi’ are not available for package ‘biomaRt’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/biomaRt’ ERROR: dependencies ‘IRanges’, ‘XVector’, ‘zlibbioc’ are not available for package ‘Biostrings’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/Biostrings’ ERROR: dependencies ‘scales’, ‘Hmisc’, ‘RColorBrewer’, ‘dichromat’, ‘IRanges’, ‘GenomicRanges’, ‘Biostrings’, ‘Rsamtools’, ‘GenomicAlignments’, ‘GenomicFeatures’, ‘AnnotationDbi’, ‘VariantAnnotation’ are not available for package ‘biovizBase’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/biovizBase’ * installing *source* package ‘bitops’ ... ** package ‘bitops’ successfully unpacked and MD5 sums checked ** libs sh: 1: gmake: not found ERROR: compilation failed for package ‘bitops’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/bitops’ * installing *source* package ‘brew’ ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (brew) ERROR: dependencies ‘IRanges’, ‘GenomicRanges’, ‘Biostrings’, ‘XVector’, ‘Rsamtools’ are not available for package ‘BSgenome’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/BSgenome’ * installing *source* package ‘cluster’ ... ** package ‘cluster’ successfully unpacked and MD5 sums checked ** libs sh: 1: gmake: not found ERROR: compilation failed for package ‘cluster’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/cluster’ * installing *source* package ‘codetools’ ... ** R ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (codetools) * installing *source* package ‘colorspace’ ... ** package ‘colorspace’ successfully unpacked and MD5 sums checked ** libs sh: 1: gmake: not found ERROR: compilation failed for package ‘colorspace’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/colorspace’ * installing *source* package ‘DBI’ ... ** package ‘DBI’ successfully unpacked and MD5 sums checked ** R ** inst ** preparing package for lazy loading Creating a generic function for ‘summary’ from package ‘base’ in package ‘DBI’ ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (DBI) * installing *source* package ‘dichromat’ ... ** package ‘dichromat’ successfully unpacked and MD5 sums checked ** R ** data ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (dichromat) * installing *source* package ‘digest’ ... ** package ‘digest’ successfully unpacked and MD5 sums checked ** libs sh: 1: gmake: not found ERROR: compilation failed for package ‘digest’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/digest’ ERROR: dependencies ‘foreach’, ‘iterators’ are not available for package ‘doParallel’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/doParallel’ ERROR: dependency ‘BBmisc’ is not available for package ‘fail’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/fail’ ERROR: dependency ‘iterators’ is not available for package ‘foreach’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/foreach’ * installing *source* package ‘Formula’ ... ** package ‘Formula’ successfully unpacked and MD5 sums checked ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (Formula) * installing *source* package ‘GenomeInfoDb’ ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (GenomeInfoDb) ERROR: dependencies ‘IRanges’, ‘GenomicRanges’, ‘Biostrings’, ‘Rsamtools’, ‘BSgenome’, ‘BiocParallel’ are not available for package ‘GenomicAlignments’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/GenomicAlignments’ ERROR: dependencies ‘IRanges’, ‘GenomicRanges’, ‘AnnotationDbi’, ‘RSQLite’, ‘Biostrings’, ‘rtracklayer’, ‘biomaRt’, ‘RCurl’, ‘Biobase’ are not available for package ‘GenomicFeatures’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/GenomicFeatures’ ERROR: dependencies ‘IRanges’, ‘XVector’ are not available for package ‘GenomicRanges’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/GenomicRanges’ ERROR: dependencies ‘ggplot2’, ‘biovizBase’, ‘reshape2’, ‘gtable’, ‘Biobase’, ‘IRanges’, ‘GenomicRanges’, ‘GenomicFeatures’, ‘Rsamtools’, ‘GenomicAlignments’, ‘BSgenome’, ‘gridExtra’, ‘scales’, ‘VariantAnnotation’, ‘Hmisc’, ‘rtracklayer’, ‘Biostrings’ are not available for package ‘ggbio’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/ggbio’ ERROR: dependencies ‘plyr’, ‘digest’, ‘gtable’, ‘reshape2’, ‘scales’, ‘proto’ are not available for package ‘ggplot2’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/ggplot2’ * installing *source* package ‘gridBase’ ... ** package ‘gridBase’ successfully unpacked and MD5 sums checked ** R ** demo ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (gridBase) * installing *source* package ‘gridExtra’ ... ** package ‘gridExtra’ successfully unpacked and MD5 sums checked ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (gridExtra) * installing *source* package ‘gtable’ ... ** package ‘gtable’ successfully unpacked and MD5 sums checked ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (gtable) * installing *source* package ‘gtools’ ... ** package ‘gtools’ successfully unpacked and MD5 sums checked ** libs sh: 1: gmake: not found ERROR: compilation failed for package ‘gtools’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/gtools’ ERROR: dependency ‘latticeExtra’ is not available for package ‘Hmisc’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/Hmisc’ * installing *source* package ‘IRanges’ ... ** libs sh: 1: gmake: not found ERROR: compilation failed for package ‘IRanges’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/IRanges’ * installing *source* package ‘iterators’ ... ** package ‘iterators’ successfully unpacked and MD5 sums checked ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ‘iterators.Rnw’ ‘writing.Rnw’ ** testing if installed package can be loaded * DONE (iterators) * installing *source* package ‘labeling’ ... ** package ‘labeling’ successfully unpacked and MD5 sums checked ** R ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (labeling) * installing *source* package ‘lattice’ ... ** package ‘lattice’ successfully unpacked and MD5 sums checked ** libs sh: 1: gmake: not found ERROR: compilation failed for package ‘lattice’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/lattice’ ERROR: dependency ‘RColorBrewer’ is not available for package ‘latticeExtra’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/latticeExtra’ * installing *source* package ‘MASS’ ... ** package ‘MASS’ successfully unpacked and MD5 sums checked ** libs sh: 1: gmake: not found ERROR: compilation failed for package ‘MASS’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/MASS’ ERROR: dependency ‘colorspace’ is not available for package ‘munsell’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/munsell’ ERROR: dependencies ‘pkgmaker’, ‘registry’, ‘rngtools’, ‘stringr’, ‘digest’, ‘colorspace’, ‘RColorBrewer’, ‘foreach’, ‘doParallel’, ‘ggplot2’, ‘reshape2’ are not available for package ‘NMF’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/NMF’ ERROR: dependencies ‘Biobase’, ‘Rcpp’ are not available for package ‘pcaMethods’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/pcaMethods’ ERROR: dependencies ‘registry’, ‘digest’, ‘stringr’, ‘xtable’ are not available for package ‘pkgmaker’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/pkgmaker’ ERROR: dependency ‘Rcpp’ is not available for package ‘plyr’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/plyr’ * installing *source* package ‘proto’ ... ** package ‘proto’ successfully unpacked and MD5 sums checked ** R ** demo ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ‘proto.Rnw’ ‘protoref.Rnw’ ** testing if installed package can be loaded * DONE (proto) * installing *source* package ‘RColorBrewer’ ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (RColorBrewer) * installing *source* package ‘Rcpp’ ... ** package ‘Rcpp’ successfully unpacked and MD5 sums checked ** libs sh: 1: gmake: not found ERROR: compilation failed for package ‘Rcpp’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/Rcpp’ ERROR: dependency ‘bitops’ is not available for package ‘RCurl’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/RCurl’ * installing *source* package ‘registry’ ... ** package ‘registry’ successfully unpacked and MD5 sums checked ** R ** demo ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ‘registry.Rnw’ using ‘UTF-8’ ** testing if installed package can be loaded * DONE (registry) ERROR: dependencies ‘plyr’, ‘stringr’ are not available for package ‘reshape2’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/reshape2’ ERROR: dependencies ‘pkgmaker’, ‘stringr’, ‘digest’ are not available for package ‘rngtools’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/rngtools’ ERROR: dependencies ‘IRanges’, ‘GenomicRanges’, ‘XVector’, ‘Biostrings’, ‘zlibbioc’, ‘bitops’ are not available for package ‘Rsamtools’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/Rsamtools’ * installing *source* package ‘RSQLite’ ... ** package ‘RSQLite’ successfully unpacked and MD5 sums checked /usr/local/lib/R/bin/config: 1: eval: gmake: not found /usr/local/lib/R/bin/config: 1: eval: gmake: not found /usr/local/lib/R/bin/config: 1: eval: gmake: not found /usr/local/lib/R/bin/config: 1: eval: gmake: not found /usr/local/lib/R/bin/config: 1: eval: gmake: not found /usr/local/lib/R/bin/config: 1: eval: gmake: not found /usr/local/lib/R/bin/config: 1: eval: gmake: not found /usr/local/lib/R/bin/config: 1: eval: gmake: not found /usr/local/lib/R/bin/config: 1: eval: gmake: not found /usr/local/lib/R/bin/config: 1: eval: gmake: not found checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -E checking for gcc... (cached) gcc checking whether we are using the GNU C compiler... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to accept ISO C89... (cached) none needed checking for library containing fdatasync... none required configure: creating ./config.status config.status: creating src/Makevars ** libs sh: 1: gmake: not found ERROR: compilation failed for package ‘RSQLite’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/RSQLite’ ERROR: dependencies ‘GenomicRanges’, ‘XML’, ‘IRanges’, ‘XVector’, ‘Biostrings’, ‘BSgenome’, ‘zlibbioc’, ‘RCurl’, ‘Rsamtools’, ‘GenomicAlignments’ are not available for package ‘rtracklayer’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/rtracklayer’ ERROR: dependencies ‘stringr’, ‘munsell’, ‘plyr’ are not available for package ‘scales’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/scales’ ERROR: dependency ‘base64enc’ is not available for package ‘sendmailR’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/sendmailR’ ERROR: dependencies ‘GenomicRanges’, ‘IRanges’, ‘VariantAnnotation’, ‘Biostrings’, ‘ggplot2’, ‘ggbio’, ‘stringr’, ‘reshape2’, ‘NMF’, ‘pcaMethods’, ‘gtools’ are not available for package ‘SomaticSignatures’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/SomaticSignatures’ * installing *source* package ‘stringr’ ... ** package ‘stringr’ successfully unpacked and MD5 sums checked ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (stringr) * installing *source* package ‘survival’ ... ** package ‘survival’ successfully unpacked and MD5 sums checked ** libs sh: 1: gmake: not found ERROR: compilation failed for package ‘survival’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/survival’ ERROR: dependencies ‘GenomicRanges’, ‘Rsamtools’, ‘IRanges’, ‘XVector’, ‘Biostrings’, ‘Biobase’, ‘AnnotationDbi’, ‘zlibbioc’, ‘BSgenome’, ‘GenomicFeatures’, ‘rtracklayer’ are not available for package ‘VariantAnnotation’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/VariantAnnotation’ * installing *source* package ‘XML’ ... ** package ‘XML’ successfully unpacked and MD5 sums checked checking for gcc... gcc checking for C compiler default output file name... rm: cannot remove `a.out.dSYM': Is a directory a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -E checking for sed... /bin/sed checking for pkg-config... /usr/bin/pkg-config checking for xml2-config... /usr/bin/xml2-config USE_XML2 = yes SED_EXTENDED_ARG: -E Minor 7, Patch 8 for 2.7.8 Located parser file -I/usr/include/libxml2/parser.h Checking for 1.8: -I/usr/include/libxml2 Using libxml2.* checking for gzopen in -lz... yes checking for xmlParseFile in -lxml2... yes checking for xmlHashSize in -lxml2... yes Using built-in xmlHashSize Checking DTD parsing (presence of externalSubset)... checking for xmlHashSize in -lxml2... yes Found xmlHashSize checking for xmlOutputBufferCreateBuffer in -lxml2... yes have xmlOutputBufferCreateBuffer() checking for xmlDocDumpFormatMemoryEnc in -lxml2... yes checking libxml/xmlversion.h usability... yes checking libxml/xmlversion.h presence... yes checking for libxml/xmlversion.h... yes Expat: FALSE Checking for return type of xmlHashScan element routine. No return value for xmlHashScan xmlNs has a context field Checking for cetype_t enumeration Using recent version of R with cetype_t enumeration type for encoding checking for xmlsec1-config... no nodegc default xml-debug default Version has XML_WITH_ZLIB Version has xmlHasFeature() **************************************** Configuration information: Libxml settings libxml include directory: -I/usr/include/libxml2 libxml library directory: -L/usr/lib/i386-linux-gnu -lxml2 -lz -lxml2 libxml 2: -DLIBXML2=1 Compilation flags: -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 Link flags: -L/usr/lib/i386-linux-gnu -lxml2 -lz -lxml2 **************************************** configure: creating ./config.status config.status: creating src/Makevars config.status: creating R/supports.R config.status: creating inst/scripts/RSXML.csh config.status: creating inst/scripts/RSXML.bsh ** libs sh: 1: gmake: not found ERROR: compilation failed for package ‘XML’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/XML’ * installing *source* package ‘xtable’ ... ** package ‘xtable’ successfully unpacked and MD5 sums checked ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (xtable) ERROR: dependency ‘IRanges’ is not available for package ‘XVector’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/XVector’ * installing *source* package ‘zlibbioc’ ... configure: creating ./config.status config.status: creating src/Makevars ** libs sh: 1: gmake: not found ERROR: compilation failed for package ‘zlibbioc’ * removing ‘/home/asif/R/i686-pc-linux-gnu-library/3.1/zlibbioc’ There were 48 warnings (use warnings() to see them)