############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/midasHLA_1.2.0.tar.gz && rm -rf midasHLA.buildbin-libdir && mkdir midasHLA.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=midasHLA.buildbin-libdir midasHLA_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL midasHLA_1.2.0.zip && rm midasHLA_1.2.0.tar.gz midasHLA_1.2.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 39 1724k 39 677k 0 0 1008k 0 0:00:01 --:--:-- 0:00:01 1008k 100 1724k 100 1724k 0 0 1279k 0 0:00:01 0:00:01 --:--:-- 1279k install for i386 * installing *source* package 'midasHLA' ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'midasHLA' finding HTML links ... done HWETest html LRTest html MiDAS-class html finding level-2 HTML links ... done MiDAS_tut_HLA html MiDAS_tut_KIR html MiDAS_tut_object html MiDAS_tut_pheno html aaVariationToCounts html adjustPValues html allele_frequencies html analyzeAssociations html analyzeConditionalAssociations html applyInheritanceModel html as.data.frame.MiDAS html backquote html characterMatches html checkAlleleFormat html checkColDataFormat html checkHlaCallsFormat html checkKirCallsFormat html checkKirGenesFormat html checkStatisticalModel html colnamesMatches html convertAlleleToVariable html countsToVariables html dfToExperimentMat html dict_dist_grantham html distGrantham html experimentMatToDf html filterByFrequency html filterByOmnibusGroups html filterByVariables html filterExperimentByFrequency html filterExperimentByVariables html filterListByElements html formatResults html getAAFrequencies html getAlleleResolution html getAllelesForAA html getExperimentFrequencies html getExperimentPopulationMultiplicator html getExperiments html getFrequencies html getFrequencyMask html getHlaCalls html getHlaCallsGenes html getHlaFrequencies html getHlaKirInteractions html getKIRFrequencies html getKirCalls html getObjectDetails html getOmnibusGroups html getPlaceholder html getReferenceFrequencies html getVariableAAPos html hasTidyMethod html hlaAlignmentGrantham html hlaCallsGranthamDistance html hlaCallsToCounts html hlaToAAVariation html hlaToVariable html isCharacterOrNULL html isClass html isClassOrNULL html isCountOrNULL html isCountsOrZeros html isExperimentCountsOrZeros html isExperimentInheritanceModelApplicable html isFlagOrNULL html isNumberOrNULL html isStringOrNULL html isTRUEorFALSE html iterativeLRT html iterativeModel html kableResults html kir_frequencies html lapply_tryCatch html listMiDASDictionaries html midasToWide html objectHasPlaceholder html omnibusTest html prepareMiDAS html prepareMiDAS_hla_NK_ligands html prepareMiDAS_hla_aa html prepareMiDAS_hla_alleles html prepareMiDAS_hla_custom html prepareMiDAS_hla_divergence html prepareMiDAS_hla_g_groups html prepareMiDAS_hla_het html prepareMiDAS_hla_kir_interactions html prepareMiDAS_hla_supertypes html prepareMiDAS_kir_custom html prepareMiDAS_kir_genes html prepareMiDAS_kir_haplotypes html readHlaAlignments html readHlaCalls html readKirCalls html reduceAlleleResolution html reduceHlaCalls html runMiDAS html runMiDASGetVarsFreq html stringMatches html summariseAAPosition html updateModel html validateFrequencyCutoffs html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path install for x64 * installing *source* package 'midasHLA' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'midasHLA' as midasHLA_1.2.0.zip * DONE (midasHLA) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'midasHLA' successfully unpacked and MD5 sums checked