{"action":"created","issue":{"url":"https://api.github.com/repos/HelikarLab/candis/issues/83","repository_url":"https://api.github.com/repos/HelikarLab/candis","labels_url":"https://api.github.com/repos/HelikarLab/candis/issues/83/labels{/name}","comments_url":"https://api.github.com/repos/HelikarLab/candis/issues/83/comments","events_url":"https://api.github.com/repos/HelikarLab/candis/issues/83/events","html_url":"https://github.com/HelikarLab/candis/issues/83","id":330957869,"node_id":"MDU6SXNzdWUzMzA5NTc4Njk=","number":83,"title":"Affy package not found while using importr function of rpy2.","user":{"login":"rupav","id":20624380,"node_id":"MDQ6VXNlcjIwNjI0Mzgw","avatar_url":"https://avatars0.githubusercontent.com/u/20624380?v=4","gravatar_id":"","url":"https://api.github.com/users/rupav","html_url":"https://github.com/rupav","followers_url":"https://api.github.com/users/rupav/followers","following_url":"https://api.github.com/users/rupav/following{/other_user}","gists_url":"https://api.github.com/users/rupav/gists{/gist_id}","starred_url":"https://api.github.com/users/rupav/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rupav/subscriptions","organizations_url":"https://api.github.com/users/rupav/orgs","repos_url":"https://api.github.com/users/rupav/repos","events_url":"https://api.github.com/users/rupav/events{/privacy}","received_events_url":"https://api.github.com/users/rupav/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2018-06-10T10:38:35Z","updated_at":"2018-06-10T13:54:19Z","closed_at":null,"author_association":"COLLABORATOR","body":"When running candis quickstart inpython notbook, I get following error.\r\n\r\n```\r\nRRuntimeError                             Traceback (most recent call last)\r\n<ipython-input-4-ebad1c6879e6> in <module>()\r\n----> 1 cdata.toARFF('data/sample.arff')\r\n\r\n~/opensource/candisVENV/lib/python3.6/site-packages/candis/ios/cdata/cdata.py in toARFF(self, path, express_config, verbose)\r\n    115             raise ValueError('No valid DNA microarray found.')\r\n    116         else:\r\n--> 117             importr('affy')\r\n    118 \r\n    119             robj = robjects.r('read.affybatch')\r\n\r\n~/opensource/candisVENV/lib/python3.6/site-packages/rpy2/robjects/packages.py in importr(name, lib_loc, robject_translations, signature_translation, suppress_messages, on_conflict, symbol_r2python, symbol_check_after, data)\r\n    451     if _package_has_namespace(rname, \r\n    452                               _system_file(package = rname)):\r\n--> 453         env = _get_namespace(rname)\r\n    454         version = _get_namespace_version(rname)[0]\r\n    455         exported_names = set(_get_namespace_exports(rname))\r\n\r\nRRuntimeError: Error in loadNamespace(name) : there is no package called ‘affy’\r\n```\r\n\r\nproblem is there is no `Affy` package, I found following packages availble (which doesn't include **affy**), link : [FAQs](https://cran.r-project.org/doc/FAQ/R-FAQ.html#How-can-add_002don-packages-be-used_003f) .\r\n![rpackages](https://user-images.githubusercontent.com/20624380/41200736-0e13a1b4-6cc8-11e8-9fe6-34e78960b59c.png)\r\n\r\nI could download the above pacakge with same method but not affy. Also CRAN don't have 'affy' package too.\r\n`rpy2.robjects.pacakges.importr(<package_name>)`\r\n\r\nThere is a package name `affy` in Bioconductor website , website used to search- [https://master.bioconductor.org/packages/release/BiocViews.html#___Software](https://master.bioconductor.org/packages/release/BiocViews.html#___Software). But I am not able to import using rpy2's `importr` function any of the pacakges from above list.\r\n\r\n**affy: Methods for Affymetrix Oligonucleotide Arrays**\r\n[https://master.bioconductor.org/packages/release/bioc/html/affy.html](https://master.bioconductor.org/packages/release/bioc/html/affy.html) \r\n\r\n@achillesrasquinha \r\n\r\n"},"comment":{"url":"https://api.github.com/repos/HelikarLab/candis/issues/comments/396050808","html_url":"https://github.com/HelikarLab/candis/issues/83#issuecomment-396050808","issue_url":"https://api.github.com/repos/HelikarLab/candis/issues/83","id":396050808,"node_id":"MDEyOklzc3VlQ29tbWVudDM5NjA1MDgwOA==","user":{"login":"rupav","id":20624380,"node_id":"MDQ6VXNlcjIwNjI0Mzgw","avatar_url":"https://avatars0.githubusercontent.com/u/20624380?v=4","gravatar_id":"","url":"https://api.github.com/users/rupav","html_url":"https://github.com/rupav","followers_url":"https://api.github.com/users/rupav/followers","following_url":"https://api.github.com/users/rupav/following{/other_user}","gists_url":"https://api.github.com/users/rupav/gists{/gist_id}","starred_url":"https://api.github.com/users/rupav/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rupav/subscriptions","organizations_url":"https://api.github.com/users/rupav/orgs","repos_url":"https://api.github.com/users/rupav/repos","events_url":"https://api.github.com/users/rupav/events{/privacy}","received_events_url":"https://api.github.com/users/rupav/received_events","type":"User","site_admin":false},"created_at":"2018-06-10T13:54:19Z","updated_at":"2018-06-10T13:54:19Z","author_association":"COLLABORATOR","body":"**Able to install 'affy' from above method**\r\n```\r\n>>> biocinstaller.biocLite(\"affy\")\r\n/home/rupav/opensource/candisVENV/lib/python3.6/site-packages/rpy2/rinterface/__init__.py:145: RRuntimeWarning: Installing package(s) ‘affy’\r\n\r\n  warnings.warn(x, RRuntimeWarning)\r\n/home/rupav/opensource/candisVENV/lib/python3.6/site-packages/rpy2/rinterface/__init__.py:145: RRuntimeWarning: also installing the dependencies ‘BiocGenerics’, ‘Biobase’, ‘affyio’, ‘preprocessCore’, ‘zlibbioc’\r\n\r\n\r\n  warnings.warn(x, RRuntimeWarning)\r\n/home/rupav/opensource/candisVENV/lib/python3.6/site-packages/rpy2/rinterface/__init__.py:145: RRuntimeWarning: trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/BiocGenerics_0.24.0.tar.gz'\r\n\r\n  warnings.warn(x, RRuntimeWarning)\r\n/home/rupav/opensource/candisVENV/lib/python3.6/site-packages/rpy2/rinterface/__init__.py:145: RRuntimeWarning:  length 43393 bytes (42 KB)\r\n\r\n  warnings.warn(x, RRuntimeWarning)\r\n/home/rupav/opensource/candisVENV/lib/python3.6/site-packages/rpy2/rinterface/__init__.py:145: RRuntimeWarning: downloaded 42 KB\r\n\r\n\r\n  warnings.warn(x, RRuntimeWarning)\r\n/home/rupav/opensource/candisVENV/lib/python3.6/site-packages/rpy2/rinterface/__init__.py:145: RRuntimeWarning: trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/Biobase_2.38.0.tar.gz'\r\n\r\n  warnings.warn(x, RRuntimeWarning)\r\n/home/rupav/opensource/candisVENV/lib/python3.6/site-packages/rpy2/rinterface/__init__.py:145: RRuntimeWarning:  length 1656734 bytes (1.6 MB)\r\n\r\n  warnings.warn(x, RRuntimeWarning)\r\n/home/rupav/opensource/candisVENV/lib/python3.6/site-packages/rpy2/rinterface/__init__.py:145: RRuntimeWarning: downloaded 1.6 MB\r\n\r\n\r\n  warnings.warn(x, RRuntimeWarning)\r\n/home/rupav/opensource/candisVENV/lib/python3.6/site-packages/rpy2/rinterface/__init__.py:145: RRuntimeWarning: trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/affyio_1.48.0.tar.gz'\r\n\r\n  warnings.warn(x, RRuntimeWarning)\r\n/home/rupav/opensource/candisVENV/lib/python3.6/site-packages/rpy2/rinterface/__init__.py:145: RRuntimeWarning:  length 109369 bytes (106 KB)\r\n\r\n  warnings.warn(x, RRuntimeWarning)\r\n/home/rupav/opensource/candisVENV/lib/python3.6/site-packages/rpy2/rinterface/__init__.py:145: RRuntimeWarning: downloaded 106 KB\r\n\r\n\r\n  warnings.warn(x, RRuntimeWarning)\r\n/home/rupav/opensource/candisVENV/lib/python3.6/site-packages/rpy2/rinterface/__init__.py:145: RRuntimeWarning: trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/preprocessCore_1.40.0.tar.gz'\r\n\r\n  warnings.warn(x, RRuntimeWarning)\r\n/home/rupav/opensource/candisVENV/lib/python3.6/site-packages/rpy2/rinterface/__init__.py:145: RRuntimeWarning:  length 122823 bytes (119 KB)\r\n\r\n  warnings.warn(x, RRuntimeWarning)\r\n/home/rupav/opensource/candisVENV/lib/python3.6/site-packages/rpy2/rinterface/__init__.py:145: RRuntimeWarning: downloaded 119 KB\r\n\r\n\r\n  warnings.warn(x, RRuntimeWarning)\r\n/home/rupav/opensource/candisVENV/lib/python3.6/site-packages/rpy2/rinterface/__init__.py:145: RRuntimeWarning: trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/zlibbioc_1.24.0.tar.gz'\r\n\r\n  warnings.warn(x, RRuntimeWarning)\r\n/home/rupav/opensource/candisVENV/lib/python3.6/site-packages/rpy2/rinterface/__init__.py:145: RRuntimeWarning:  length 257311 bytes (251 KB)\r\n\r\n  warnings.warn(x, RRuntimeWarning)\r\n/home/rupav/opensource/candisVENV/lib/python3.6/site-packages/rpy2/rinterface/__init__.py:145: RRuntimeWarning: downloaded 251 KB\r\n\r\n\r\n  warnings.warn(x, RRuntimeWarning)\r\n/home/rupav/opensource/candisVENV/lib/python3.6/site-packages/rpy2/rinterface/__init__.py:145: RRuntimeWarning: trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/affy_1.56.0.tar.gz'\r\n\r\n  warnings.warn(x, RRuntimeWarning)\r\n/home/rupav/opensource/candisVENV/lib/python3.6/site-packages/rpy2/rinterface/__init__.py:145: RRuntimeWarning:  length 1316772 bytes (1.3 MB)\r\n\r\n  warnings.warn(x, RRuntimeWarning)\r\n/home/rupav/opensource/candisVENV/lib/python3.6/site-packages/rpy2/rinterface/__init__.py:145: RRuntimeWarning: downloaded 1.3 MB\r\n\r\n\r\n  warnings.warn(x, RRuntimeWarning)\r\n* installing *source* package ‘BiocGenerics’ ...\r\n** R\r\n** inst\r\n** preparing package for lazy loading\r\nCreating a new generic function for ‘append’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘as.data.frame’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘cbind’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘rbind’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘do.call’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘duplicated’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘anyDuplicated’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘eval’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘pmax’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘pmin’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘pmax.int’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘pmin.int’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘Reduce’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘Filter’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘Find’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘Map’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘Position’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘get’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘mget’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘grep’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘grepl’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘is.unsorted’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘lapply’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘sapply’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘lengths’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘mapply’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘match’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘rowSums’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘colSums’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘rowMeans’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘colMeans’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘order’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘paste’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘rank’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘rownames’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘colnames’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘union’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘intersect’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘setdiff’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘sort’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘table’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘tapply’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘unique’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘unsplit’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘var’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘sd’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘which’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘which.max’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘which.min’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘IQR’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘mad’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘xtabs’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘clusterCall’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘clusterApply’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘clusterApplyLB’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘clusterEvalQ’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘clusterExport’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘clusterMap’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘parLapply’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘parSapply’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘parApply’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘parRapply’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘parCapply’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘parLapplyLB’ in package ‘BiocGenerics’\r\nCreating a new generic function for ‘parSapplyLB’ in package ‘BiocGenerics’\r\n** help\r\n*** installing help indices\r\n** building package indices\r\n** testing if installed package can be loaded\r\n* DONE (BiocGenerics)\r\n* installing *source* package ‘preprocessCore’ ...\r\nchecking for gcc... gcc -std=gnu99\r\nchecking whether the C compiler works... yes\r\nchecking for C compiler default output file name... a.out\r\nchecking for suffix of executables... \r\nchecking whether we are cross compiling... no\r\nchecking for suffix of object files... o\r\nchecking whether we are using the GNU C compiler... yes\r\nchecking whether gcc -std=gnu99 accepts -g... yes\r\nchecking for gcc -std=gnu99 option to accept ISO C89... none needed\r\nchecking how to run the C preprocessor... gcc -std=gnu99 -E\r\nchecking for library containing pthread_create... -lpthread\r\nchecking for grep that handles long lines and -e... /bin/grep\r\nchecking for egrep... /bin/grep -E\r\nchecking for ANSI C header files... yes\r\nchecking for sys/types.h... yes\r\nchecking for sys/stat.h... yes\r\nchecking for stdlib.h... yes\r\nchecking for string.h... yes\r\nchecking for memory.h... yes\r\nchecking for strings.h... yes\r\nchecking for inttypes.h... yes\r\nchecking for stdint.h... yes\r\nchecking for unistd.h... yes\r\nchecking for stdlib.h... (cached) yes\r\nchecking if PTHREAD_STACK_MIN is defined... yes\r\nconfigure: Enabling threading for preprocessCore\r\nconfigure: creating ./config.status\r\nconfig.status: creating src/Makevars\r\n** libs\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DPACKAGE_NAME=\\\"\\\" -DPACKAGE_TARNAME=\\\"\\\" -DPACKAGE_VERSION=\\\"\\\" -DPACKAGE_STRING=\\\"\\\" -DPACKAGE_BUGREPORT=\\\"\\\" -DPACKAGE_URL=\\\"\\\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_colSummarize.c -o R_colSummarize.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DPACKAGE_NAME=\\\"\\\" -DPACKAGE_TARNAME=\\\"\\\" -DPACKAGE_VERSION=\\\"\\\" -DPACKAGE_STRING=\\\"\\\" -DPACKAGE_BUGREPORT=\\\"\\\" -DPACKAGE_URL=\\\"\\\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_plmd_interfaces.c -o R_plmd_interfaces.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DPACKAGE_NAME=\\\"\\\" -DPACKAGE_TARNAME=\\\"\\\" -DPACKAGE_VERSION=\\\"\\\" -DPACKAGE_STRING=\\\"\\\" -DPACKAGE_BUGREPORT=\\\"\\\" -DPACKAGE_URL=\\\"\\\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_plmr_interfaces.c -o R_plmr_interfaces.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DPACKAGE_NAME=\\\"\\\" -DPACKAGE_TARNAME=\\\"\\\" -DPACKAGE_VERSION=\\\"\\\" -DPACKAGE_STRING=\\\"\\\" -DPACKAGE_BUGREPORT=\\\"\\\" -DPACKAGE_URL=\\\"\\\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_rlm_interfaces.c -o R_rlm_interfaces.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DPACKAGE_NAME=\\\"\\\" -DPACKAGE_TARNAME=\\\"\\\" -DPACKAGE_VERSION=\\\"\\\" -DPACKAGE_STRING=\\\"\\\" -DPACKAGE_BUGREPORT=\\\"\\\" -DPACKAGE_URL=\\\"\\\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_subColSummarize.c -o R_subColSummarize.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DPACKAGE_NAME=\\\"\\\" -DPACKAGE_TARNAME=\\\"\\\" -DPACKAGE_VERSION=\\\"\\\" -DPACKAGE_STRING=\\\"\\\" -DPACKAGE_BUGREPORT=\\\"\\\" -DPACKAGE_URL=\\\"\\\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_subrcModel_interfaces.c -o R_subrcModel_interfaces.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DPACKAGE_NAME=\\\"\\\" -DPACKAGE_TARNAME=\\\"\\\" -DPACKAGE_VERSION=\\\"\\\" -DPACKAGE_STRING=\\\"\\\" -DPACKAGE_BUGREPORT=\\\"\\\" -DPACKAGE_URL=\\\"\\\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c avg.c -o avg.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DPACKAGE_NAME=\\\"\\\" -DPACKAGE_TARNAME=\\\"\\\" -DPACKAGE_VERSION=\\\"\\\" -DPACKAGE_STRING=\\\"\\\" -DPACKAGE_BUGREPORT=\\\"\\\" -DPACKAGE_URL=\\\"\\\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c avg_log.c -o avg_log.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DPACKAGE_NAME=\\\"\\\" -DPACKAGE_TARNAME=\\\"\\\" -DPACKAGE_VERSION=\\\"\\\" -DPACKAGE_STRING=\\\"\\\" -DPACKAGE_BUGREPORT=\\\"\\\" -DPACKAGE_URL=\\\"\\\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c biweight.c -o biweight.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DPACKAGE_NAME=\\\"\\\" -DPACKAGE_TARNAME=\\\"\\\" -DPACKAGE_VERSION=\\\"\\\" -DPACKAGE_STRING=\\\"\\\" -DPACKAGE_BUGREPORT=\\\"\\\" -DPACKAGE_URL=\\\"\\\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init_package.c -o init_package.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DPACKAGE_NAME=\\\"\\\" -DPACKAGE_TARNAME=\\\"\\\" -DPACKAGE_VERSION=\\\"\\\" -DPACKAGE_STRING=\\\"\\\" -DPACKAGE_BUGREPORT=\\\"\\\" -DPACKAGE_URL=\\\"\\\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c lm.c -o lm.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DPACKAGE_NAME=\\\"\\\" -DPACKAGE_TARNAME=\\\"\\\" -DPACKAGE_VERSION=\\\"\\\" -DPACKAGE_STRING=\\\"\\\" -DPACKAGE_BUGREPORT=\\\"\\\" -DPACKAGE_URL=\\\"\\\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c log_avg.c -o log_avg.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DPACKAGE_NAME=\\\"\\\" -DPACKAGE_TARNAME=\\\"\\\" -DPACKAGE_VERSION=\\\"\\\" -DPACKAGE_STRING=\\\"\\\" -DPACKAGE_BUGREPORT=\\\"\\\" -DPACKAGE_URL=\\\"\\\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c log_median.c -o log_median.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DPACKAGE_NAME=\\\"\\\" -DPACKAGE_TARNAME=\\\"\\\" -DPACKAGE_VERSION=\\\"\\\" -DPACKAGE_STRING=\\\"\\\" -DPACKAGE_BUGREPORT=\\\"\\\" -DPACKAGE_URL=\\\"\\\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c matrix_functions.c -o matrix_functions.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DPACKAGE_NAME=\\\"\\\" -DPACKAGE_TARNAME=\\\"\\\" -DPACKAGE_VERSION=\\\"\\\" -DPACKAGE_STRING=\\\"\\\" -DPACKAGE_BUGREPORT=\\\"\\\" -DPACKAGE_URL=\\\"\\\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c median.c -o median.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DPACKAGE_NAME=\\\"\\\" -DPACKAGE_TARNAME=\\\"\\\" -DPACKAGE_VERSION=\\\"\\\" -DPACKAGE_STRING=\\\"\\\" -DPACKAGE_BUGREPORT=\\\"\\\" -DPACKAGE_URL=\\\"\\\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c median_log.c -o median_log.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DPACKAGE_NAME=\\\"\\\" -DPACKAGE_TARNAME=\\\"\\\" -DPACKAGE_VERSION=\\\"\\\" -DPACKAGE_STRING=\\\"\\\" -DPACKAGE_BUGREPORT=\\\"\\\" -DPACKAGE_URL=\\\"\\\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c medianpolish.c -o medianpolish.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DPACKAGE_NAME=\\\"\\\" -DPACKAGE_TARNAME=\\\"\\\" -DPACKAGE_VERSION=\\\"\\\" -DPACKAGE_STRING=\\\"\\\" -DPACKAGE_BUGREPORT=\\\"\\\" -DPACKAGE_URL=\\\"\\\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c plmd.c -o plmd.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DPACKAGE_NAME=\\\"\\\" -DPACKAGE_TARNAME=\\\"\\\" -DPACKAGE_VERSION=\\\"\\\" -DPACKAGE_STRING=\\\"\\\" -DPACKAGE_BUGREPORT=\\\"\\\" -DPACKAGE_URL=\\\"\\\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c plmr.c -o plmr.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DPACKAGE_NAME=\\\"\\\" -DPACKAGE_TARNAME=\\\"\\\" -DPACKAGE_VERSION=\\\"\\\" -DPACKAGE_STRING=\\\"\\\" -DPACKAGE_BUGREPORT=\\\"\\\" -DPACKAGE_URL=\\\"\\\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c psi_fns.c -o psi_fns.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DPACKAGE_NAME=\\\"\\\" -DPACKAGE_TARNAME=\\\"\\\" -DPACKAGE_VERSION=\\\"\\\" -DPACKAGE_STRING=\\\"\\\" -DPACKAGE_BUGREPORT=\\\"\\\" -DPACKAGE_URL=\\\"\\\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c qnorm.c -o qnorm.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DPACKAGE_NAME=\\\"\\\" -DPACKAGE_TARNAME=\\\"\\\" -DPACKAGE_VERSION=\\\"\\\" -DPACKAGE_STRING=\\\"\\\" -DPACKAGE_BUGREPORT=\\\"\\\" -DPACKAGE_URL=\\\"\\\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rlm.c -o rlm.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DPACKAGE_NAME=\\\"\\\" -DPACKAGE_TARNAME=\\\"\\\" -DPACKAGE_VERSION=\\\"\\\" -DPACKAGE_STRING=\\\"\\\" -DPACKAGE_BUGREPORT=\\\"\\\" -DPACKAGE_URL=\\\"\\\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rlm_anova.c -o rlm_anova.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DPACKAGE_NAME=\\\"\\\" -DPACKAGE_TARNAME=\\\"\\\" -DPACKAGE_VERSION=\\\"\\\" -DPACKAGE_STRING=\\\"\\\" -DPACKAGE_BUGREPORT=\\\"\\\" -DPACKAGE_URL=\\\"\\\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rlm_se.c -o rlm_se.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DPACKAGE_NAME=\\\"\\\" -DPACKAGE_TARNAME=\\\"\\\" -DPACKAGE_VERSION=\\\"\\\" -DPACKAGE_STRING=\\\"\\\" -DPACKAGE_BUGREPORT=\\\"\\\" -DPACKAGE_URL=\\\"\\\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rma_background4.c -o rma_background4.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DPACKAGE_NAME=\\\"\\\" -DPACKAGE_TARNAME=\\\"\\\" -DPACKAGE_VERSION=\\\"\\\" -DPACKAGE_STRING=\\\"\\\" -DPACKAGE_BUGREPORT=\\\"\\\" -DPACKAGE_URL=\\\"\\\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rma_common.c -o rma_common.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -DPACKAGE_NAME=\\\"\\\" -DPACKAGE_TARNAME=\\\"\\\" -DPACKAGE_VERSION=\\\"\\\" -DPACKAGE_STRING=\\\"\\\" -DPACKAGE_BUGREPORT=\\\"\\\" -DPACKAGE_URL=\\\"\\\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_STDLIB_H=1 -DUSE_PTHREADS=1 -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c weightedkerneldensity.c -o weightedkerneldensity.o\r\ng++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o preprocessCore.so R_colSummarize.o R_plmd_interfaces.o R_plmr_interfaces.o R_rlm_interfaces.o R_subColSummarize.o R_subrcModel_interfaces.o avg.o avg_log.o biweight.o init_package.o lm.o log_avg.o log_median.o matrix_functions.o median.o median_log.o medianpolish.o plmd.o plmr.o psi_fns.o qnorm.o rlm.o rlm_anova.o rlm_se.o rma_background4.o rma_common.o weightedkerneldensity.o -lpthread -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR\r\ninstalling to /home/rupav/R/x86_64-pc-linux-gnu-library/3.4/preprocessCore/libs\r\n** R\r\n** inst\r\n** preparing package for lazy loading\r\n** help\r\n*** installing help indices\r\n** building package indices\r\n** testing if installed package can be loaded\r\n* DONE (preprocessCore)\r\n* installing *source* package ‘zlibbioc’ ...\r\nconfigure: creating ./config.status\r\nconfig.status: creating src/Makevars\r\n** libs\r\nmkdir -p \"/home/rupav/R/x86_64-pc-linux-gnu-library/3.4/zlibbioc/include\"\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_init_zlibbioc.c -o R_init_zlibbioc.o\r\ng++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o zlibbioc.so R_init_zlibbioc.o -L/usr/lib/R/lib -lR\r\ninstalling to /home/rupav/R/x86_64-pc-linux-gnu-library/3.4/zlibbioc/libs\r\n** R\r\n** inst\r\n** preparing package for lazy loading\r\n** help\r\n*** installing help indices\r\n** building package indices\r\n** installing vignettes\r\n** testing if installed package can be loaded\r\n* DONE (zlibbioc)\r\n* installing *source* package ‘Biobase’ ...\r\n** libs\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Rinit.c -o Rinit.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c anyMissing.c -o anyMissing.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c envir.c -o envir.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c matchpt.c -o matchpt.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rowMedians.c -o rowMedians.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c sublist_extract.c -o sublist_extract.o\r\ng++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o Biobase.so Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o -L/usr/lib/R/lib -lR\r\ninstalling to /home/rupav/R/x86_64-pc-linux-gnu-library/3.4/Biobase/libs\r\n** R\r\n** data\r\n** inst\r\n** preparing package for lazy loading\r\n** help\r\n*** installing help indices\r\n** building package indices\r\n** installing vignettes\r\n** testing if installed package can be loaded\r\n* DONE (Biobase)\r\n* installing *source* package ‘affyio’ ...\r\nchecking for gcc... gcc\r\nchecking whether the C compiler works... yes\r\nchecking for C compiler default output file name... a.out\r\nchecking for suffix of executables... \r\nchecking whether we are cross compiling... no\r\nchecking for suffix of object files... o\r\nchecking whether we are using the GNU C compiler... yes\r\nchecking whether gcc accepts -g... yes\r\nchecking for gcc option to accept ISO C89... none needed\r\nchecking how to run the C preprocessor... gcc -E\r\nchecking for grep that handles long lines and -e... /bin/grep\r\nchecking for egrep... /bin/grep -E\r\nchecking for ANSI C header files... yes\r\nchecking for sys/types.h... yes\r\nchecking for sys/stat.h... yes\r\nchecking for stdlib.h... yes\r\nchecking for string.h... yes\r\nchecking for memory.h... yes\r\nchecking for strings.h... yes\r\nchecking for inttypes.h... yes\r\nchecking for stdint.h... yes\r\nchecking for unistd.h... yes\r\nchecking for main in -lz... yes\r\nchecking zlib.h usability... yes\r\nchecking zlib.h presence... yes\r\nchecking for zlib.h... yes\r\nchecking if zlib version >= 1.1.3... yes\r\nchecking for pthread_create in -lpthread... yes\r\nchecking if we can use pthreads... yes\r\nchecking if PTHREAD_STACK_MIN is defined... yes\r\nconfigure: Enabling threading for affyio\r\nconfigure: creating ./config.status\r\nconfig.status: creating src/Makevars\r\n** libs\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPACKAGE_NAME=\\\"\\\" -DPACKAGE_TARNAME=\\\"\\\" -DPACKAGE_VERSION=\\\"\\\" -DPACKAGE_STRING=\\\"\\\" -DPACKAGE_BUGREPORT=\\\"\\\" -DPACKAGE_URL=\\\"\\\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1    -g -O2   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c fread_functions.c -o fread_functions.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPACKAGE_NAME=\\\"\\\" -DPACKAGE_TARNAME=\\\"\\\" -DPACKAGE_VERSION=\\\"\\\" -DPACKAGE_STRING=\\\"\\\" -DPACKAGE_BUGREPORT=\\\"\\\" -DPACKAGE_URL=\\\"\\\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1    -g -O2   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init_package.c -o init_package.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPACKAGE_NAME=\\\"\\\" -DPACKAGE_TARNAME=\\\"\\\" -DPACKAGE_VERSION=\\\"\\\" -DPACKAGE_STRING=\\\"\\\" -DPACKAGE_BUGREPORT=\\\"\\\" -DPACKAGE_URL=\\\"\\\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1    -g -O2   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c read_abatch.c -o read_abatch.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPACKAGE_NAME=\\\"\\\" -DPACKAGE_TARNAME=\\\"\\\" -DPACKAGE_VERSION=\\\"\\\" -DPACKAGE_STRING=\\\"\\\" -DPACKAGE_BUGREPORT=\\\"\\\" -DPACKAGE_URL=\\\"\\\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1    -g -O2   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c read_bpmap.c -o read_bpmap.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPACKAGE_NAME=\\\"\\\" -DPACKAGE_TARNAME=\\\"\\\" -DPACKAGE_VERSION=\\\"\\\" -DPACKAGE_STRING=\\\"\\\" -DPACKAGE_BUGREPORT=\\\"\\\" -DPACKAGE_URL=\\\"\\\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1    -g -O2   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c read_cdf_xda.c -o read_cdf_xda.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPACKAGE_NAME=\\\"\\\" -DPACKAGE_TARNAME=\\\"\\\" -DPACKAGE_VERSION=\\\"\\\" -DPACKAGE_STRING=\\\"\\\" -DPACKAGE_BUGREPORT=\\\"\\\" -DPACKAGE_URL=\\\"\\\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1    -g -O2   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c read_cdffile2.c -o read_cdffile2.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPACKAGE_NAME=\\\"\\\" -DPACKAGE_TARNAME=\\\"\\\" -DPACKAGE_VERSION=\\\"\\\" -DPACKAGE_STRING=\\\"\\\" -DPACKAGE_BUGREPORT=\\\"\\\" -DPACKAGE_URL=\\\"\\\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1    -g -O2   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c read_celfile_generic.c -o read_celfile_generic.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPACKAGE_NAME=\\\"\\\" -DPACKAGE_TARNAME=\\\"\\\" -DPACKAGE_VERSION=\\\"\\\" -DPACKAGE_STRING=\\\"\\\" -DPACKAGE_BUGREPORT=\\\"\\\" -DPACKAGE_URL=\\\"\\\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1    -g -O2   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c read_clf.c -o read_clf.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPACKAGE_NAME=\\\"\\\" -DPACKAGE_TARNAME=\\\"\\\" -DPACKAGE_VERSION=\\\"\\\" -DPACKAGE_STRING=\\\"\\\" -DPACKAGE_BUGREPORT=\\\"\\\" -DPACKAGE_URL=\\\"\\\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1    -g -O2   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c read_generic.c -o read_generic.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPACKAGE_NAME=\\\"\\\" -DPACKAGE_TARNAME=\\\"\\\" -DPACKAGE_VERSION=\\\"\\\" -DPACKAGE_STRING=\\\"\\\" -DPACKAGE_BUGREPORT=\\\"\\\" -DPACKAGE_URL=\\\"\\\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1    -g -O2   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c read_multichannel_celfile_generic.c -o read_multichannel_celfile_generic.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPACKAGE_NAME=\\\"\\\" -DPACKAGE_TARNAME=\\\"\\\" -DPACKAGE_VERSION=\\\"\\\" -DPACKAGE_STRING=\\\"\\\" -DPACKAGE_BUGREPORT=\\\"\\\" -DPACKAGE_URL=\\\"\\\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1    -g -O2   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c read_pgf.c -o read_pgf.o\r\nread_pgf.c: In function ‘pgf_count_probeset_types’:\r\nread_pgf.c:1265:28: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]\r\n  my_pgf->probesets->current= my_pgf->probesets->current->next;\r\n                            ^\r\ng++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o affyio.so fread_functions.o init_package.o read_abatch.o read_bpmap.o read_cdf_xda.o read_cdffile2.o read_celfile_generic.o read_clf.o read_generic.o read_multichannel_celfile_generic.o read_pgf.o -lpthread -lz -L/usr/lib/R/lib -lR\r\ninstalling to /home/rupav/R/x86_64-pc-linux-gnu-library/3.4/affyio/libs\r\n** R\r\n** preparing package for lazy loading\r\n** help\r\n*** installing help indices\r\n** building package indices\r\n** testing if installed package can be loaded\r\n* DONE (affyio)\r\n* installing *source* package ‘affy’ ...\r\ncreating cache ./config.cache\r\nchecking how to run the C preprocessor... cc -E\r\nchecking for main in -lz... yes\r\nchecking for zlib.h... yes\r\nchecking if zlib version >= 1.1.3... yes\r\nupdating cache ./config.cache\r\ncreating ./config.status\r\ncreating src/Makevars\r\n** libs\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DHAVE_ZLIB=1  -I\"/home/rupav/R/x86_64-pc-linux-gnu-library/3.4/preprocessCore/include\"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c chipbackground.c -o chipbackground.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DHAVE_ZLIB=1  -I\"/home/rupav/R/x86_64-pc-linux-gnu-library/3.4/preprocessCore/include\"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c getall_locations.c -o getall_locations.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DHAVE_ZLIB=1  -I\"/home/rupav/R/x86_64-pc-linux-gnu-library/3.4/preprocessCore/include\"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mas5calls.c -o mas5calls.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DHAVE_ZLIB=1  -I\"/home/rupav/R/x86_64-pc-linux-gnu-library/3.4/preprocessCore/include\"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rma2.c -o rma2.o\r\ngcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DHAVE_ZLIB=1  -I\"/home/rupav/R/x86_64-pc-linux-gnu-library/3.4/preprocessCore/include\"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Oe9izK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rma_common.c -o rma_common.o\r\ng++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o affy.so chipbackground.o getall_locations.o mas5calls.o rma2.o rma_common.o -lz -L/usr/lib/R/lib -lR\r\ninstalling to /home/rupav/R/x86_64-pc-linux-gnu-library/3.4/affy/libs\r\n** R\r\n** data\r\n** demo\r\n** inst\r\n** preparing package for lazy loading\r\n** help\r\n*** installing help indices\r\n** building package indices\r\n** installing vignettes\r\n** testing if installed package can be loaded\r\n* DONE (affy)\r\nR object with classes: ('character',) mapped to:\r\n<StrVector - Python:0x7fa96dd7f988 / R:0x6d31318>\r\n['affy']\r\n\r\n```"}}
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