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Problems installing BioC, zlib.h

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Markus Schmidberger ▴ 380

@markus-schmidberger-2240

Last seen 9.6 years ago

Hello, we have installed R-2.5.0 at a Debian 4.0 ./configure --with-x=no && make && make checks && make install There are no problems and R is running very well. >sessionInfo() R version 2.5.0 (2007-04-23) i686-pc-linux-gnu locale: LC_CTYPE=de_DE.UTF-8;LC_NUMERIC=C;LC_TIME=de_DE.UTF-8;LC_COLLATE=de_DE .UTF-8;LC_MONETARY=de_DE.UTF-8;LC_MESSAGES=de_DE.UTF-8;LC_PAPER=de_DE. UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=de_DE.UTF-8 ;LC_IDENTIFICATION=C attached base packages: [1] "stats" "graphics" "grDevices" "utils" "datasets" "methods" [7] "base" But when we install Bioconductor or only the library(affyio) we get the error: ================================================== downloaded 57Kb * Installing *source* package 'affyio' ... creating cache ./config.cache checking how to run the C preprocessor... cc -E checking for main in -lz... no updating cache ./config.cache creating ./config.status creating src/Makevars ** libs gcc -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/lib/R/include -I/usr/local/include -fpic -g -O2 -c read_abatch.c -o read_abatch.o read_abatch.c:153:18: error: zlib.h: Datei oder Verzeichnis nicht gefunden read_abatch.c:1246: error: expected declaration specifiers or ?...? before ?gzFile? read_abatch.c: In function ?ReadgzFileLine?: read_abatch.c:1247: warning: implicit declaration of function ?gzgets? read_abatch.c:1247: error: ?currentFile? undeclared (first use in this function) read_abatch.c:1247: error: (Each undeclared identifier is reported only once I think that there is missing a zlib library, but zlib-bin and zlibc are installed. What is wrong? Thanks a lot Markus -- Dipl.-Tech. Math. Markus Schmidberger Ludwig-Maximilians-Universit?t M?nchen IBE - Institut f?r medizinische Informationsverarbeitung, Biometrie und Epidemiologie Marchioninistr. 15, D-81377 Muenchen URL: http://ibe.web.med.uni-muenchen.de Mail: Markus.Schmidberger [at] ibe.med.uni-muenchen.de

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ADD COMMENT • link updated 16.8 years ago by Laurent Gatto 1.6k • written 16.8 years ago by Markus Schmidberger ▴ 380

score 0 · Answer 1 · 2007-06-26

Hi Markus, Markus Schmidberger wrote: > Hello, > > we have installed R-2.5.0 at a Debian 4.0 > ./configure --with-x=no && make && make checks && make install > > There are no problems and R is running very well. > >sessionInfo() > R version 2.5.0 (2007-04-23) > i686-pc-linux-gnu > locale: > LC_CTYPE=de_DE.UTF-8;LC_NUMERIC=C;LC_TIME=de_DE.UTF-8;LC_COLLATE=de_ DE.UTF-8;LC_MONETARY=de_DE.UTF-8;LC_MESSAGES=de_DE.UTF-8;LC_PAPER=de_D E.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=de_DE.UTF -8;LC_IDENTIFICATION=C > > attached base packages: > [1] "stats" "graphics" "grDevices" "utils" "datasets" "methods" > [7] "base" > > But when we install Bioconductor or only the library(affyio) we get the > error: > ================================================== > downloaded 57Kb > * Installing *source* package 'affyio' ... > creating cache ./config.cache > checking how to run the C preprocessor... cc -E > checking for main in -lz... no > updating cache ./config.cache > creating ./config.status > creating src/Makevars > ** libs > gcc -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/lib/R/include > -I/usr/local/include -fpic -g -O2 -c read_abatch.c -o read_abatch.o > read_abatch.c:153:18: error: zlib.h: Datei oder Verzeichnis nicht gefunden > read_abatch.c:1246: error: expected declaration specifiers or ?...? > before ?gzFile? > read_abatch.c: In function ?ReadgzFileLine?: > read_abatch.c:1247: warning: implicit declaration of function ?gzgets? > read_abatch.c:1247: error: ?currentFile? undeclared (first use in this > function) > read_abatch.c:1247: error: (Each undeclared identifier is reported only > once > > I think that there is missing a zlib library, but zlib-bin and zlibc are > installed. affyio configure script is reporting "checking for main in -lz... no" which seems to indicate that something is wrong with your zlib installation. Try this simple test (1): echo "main() {return 0;}" | gcc -x c - -lz This should produce an executable a.out linked to the libz library. If you are curious to see which libs a.out is actually linked to, try (2): ldd a.out If (1) fails for you, then you probably have the wrong deb packages installed or something bad happened when they were installed. Try to reinstall them. FYI, on my Ubuntu 6.06 system, the zlib packages I have are zlib1g and zlib1g-dev The latter is required too in order to compile affyio. Cheers, H. > What is wrong? > > Thanks a lot > Markus >

score 0 · Answer 2 · 2007-06-26

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Laurent Gatto 1.6k

@laurent-gatto-5645

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Belgium

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ADD COMMENT • link 16.8 years ago Laurent Gatto 1.6k

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Thanks, thats it! zlib1g-dev was missing Markus Laurent Gatto schrieb: > Hi Markus, > > I think that you need to install > - zlib1g (compression library - runtime) and > - zlib1g-dev (compression library - development). > > Laurent > > -- > Laurent Gatto > DNAVision SA > > > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch on behalf of Markus Schmidberger > Sent: Tue 26/06/2007 18:10 > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] Problems installing BioC, zlib.h > > Hello, > > we have installed R-2.5.0 at a Debian 4.0 > ./configure --with-x=no && make && make checks && make install > > There are no problems and R is running very well. > >sessionInfo() > R version 2.5.0 (2007-04-23) > i686-pc-linux-gnu > locale: > LC_CTYPE=de_DE.UTF-8;LC_NUMERIC=C;LC_TIME=de_DE.UTF-8;LC_COLLATE=de_ DE.UTF-8;LC_MONETARY=de_DE.UTF-8;LC_MESSAGES=de_DE.UTF-8;LC_PAPER=de_D E.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=de_DE.UTF -8;LC_IDENTIFICATION=C > > attached base packages: > [1] "stats" "graphics" "grDevices" "utils" "datasets" "methods" > [7] "base" > > But when we install Bioconductor or only the library(affyio) we get the > error: > ================================================== > downloaded 57Kb > * Installing *source* package 'affyio' ... > creating cache ./config.cache > checking how to run the C preprocessor... cc -E > checking for main in -lz... no > updating cache ./config.cache > creating ./config.status > creating src/Makevars > ** libs > gcc -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/lib/R/include > -I/usr/local/include -fpic -g -O2 -c read_abatch.c -o read_abatch.o > read_abatch.c:153:18: error: zlib.h: Datei oder Verzeichnis nicht gefunden > read_abatch.c:1246: error: expected declaration specifiers or ?...? > before ?gzFile? > read_abatch.c: In function ?ReadgzFileLine?: > read_abatch.c:1247: warning: implicit declaration of function ?gzgets? > read_abatch.c:1247: error: ?currentFile? undeclared (first use in this > function) > read_abatch.c:1247: error: (Each undeclared identifier is reported only > once > > I think that there is missing a zlib library, but zlib-bin and zlibc are > installed. > What is wrong? > > Thanks a lot > Markus > > -- Dipl.-Tech. Math. Markus Schmidberger Ludwig-Maximilians-Universit?t M?nchen IBE - Institut f?r medizinische Informationsverarbeitung, Biometrie und Epidemiologie Marchioninistr. 15, D-81377 Muenchen URL: http://ibe.web.med.uni-muenchen.de Mail: Markus.Schmidberger [at] ibe.med.uni-muenchen.de Tel: +49 (089) 7095 - 4599

ADD REPLY • link 16.8 years ago Markus Schmidberger ▴ 380