Problems with Downloading packages

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Abbhirami Rajagopal ▴ 70

@abbhirami-rajagopal-3962

Last seen 10.2 years ago

Hi I am new to R and bioconductor, I have been trying to download the packages for flow cytometry data analysis Below is the error message I got- I had to reinstall R a few times before I got to this stage. The installation seemed to have work fine but I still cannot get the package- please HELP Regds Abi * installing *source* package flowCore ... ** libs ** arch - i386 sh: make: command not found ERROR: compilation failed for package flowCore * removing /Library/Frameworks/R.framework/Versions/2.10/Resources/library/flowC ore * restoring previous /Library/Frameworks/R.framework/Versions/2.10/Resources/library/flowC ore The downloaded packages are in /private/var/folders/32/32m0GhxDHKS- TBOPVk6WIU+++TI/-Tmp-/Rtmpdm9kpV/downloaded_packages > library(flowcore) Error in library(flowcore) : there is no package called 'flowcore' In addition: Warning message: In install.packages(c("flowCore"), lib = "/Library/Frameworks/R.framework/Resources/library/", : installation of package 'flowCore' had non-zero exit status > [[alternative HTML version deleted]]

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ADD COMMENT • link updated 14.7 years ago by Martin Morgan 25k • written 14.7 years ago by Abbhirami Rajagopal ▴ 70

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Martin Morgan 25k

@martin-morgan-1513

Last seen 4 months ago

United States

On 03/16/2010 09:40 AM, Abbhirami Rajagopal wrote: > Hi > > I am new to R and bioconductor, I have been trying to download the packages > for flow cytometry data analysis > > Below is the error message I got- I had to reinstall R a few times before I > got to this stage. The installation seemed to have work fine but I still > cannot get the package- please HELP Hi Abi -- are you installing using the instructions at http://bioconductor.org/install ? Please provide a complete transcript. Martin > > Regds > Abi > > * installing *source* package ?flowCore? ... > ** libs > ** arch - i386 > sh: make: command not found > ERROR: compilation failed for package ?flowCore? > * removing > ?/Library/Frameworks/R.framework/Versions/2.10/Resources/library/flo wCore? > * restoring previous > ?/Library/Frameworks/R.framework/Versions/2.10/Resources/library/flo wCore? > > The downloaded packages are in > ?/private/var/folders/32/32m0GhxDHKS- TBOPVk6WIU+++TI/-Tmp-/Rtmpdm9kpV/downloaded_packages? >> library(flowcore) > Error in library(flowcore) : there is no package called 'flowcore' > In addition: Warning message: > In install.packages(c("flowCore"), lib = > "/Library/Frameworks/R.framework/Resources/library/", : > installation of package 'flowCore' had non-zero exit status >> > > [[alternative HTML version deleted]] > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793

ADD COMMENT • link 14.7 years ago Martin Morgan 25k

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Sean Davis 21k

@sean-davis-490

Last seen 3 months ago

United States

On Tue, Mar 16, 2010 at 12:40 PM, Abbhirami Rajagopal <abbhirami at="" gmail.com=""> wrote: > Hi > > I am new to R and bioconductor, I have been trying to download the packages > for flow cytometry data analysis > > Below is the error message I got- I had to reinstall R a few times before I > got to this stage. The installation seemed to have work fine but I still > cannot get the package- please HELP > > Regds > Abi > > * installing *source* package ?flowCore? ... > ** libs > ** arch - i386 > sh: make: command not found > ERROR: compilation failed for package ?flowCore? Hi, Abi. This says that there was an error trying to install the package. It looks like you are on a Mac and trying to install a source package. Do you have Xcode installed, as the error also suggests that "make" was not found on your system. As an aside, it is always a good idea to include the output of sessionInfo() when reporting problems to the list. Sean > * removing > ?/Library/Frameworks/R.framework/Versions/2.10/Resources/library/flo wCore? > * restoring previous > ?/Library/Frameworks/R.framework/Versions/2.10/Resources/library/flo wCore? > > The downloaded packages are in > ?/private/var/folders/32/32m0GhxDHKS- TBOPVk6WIU+++TI/-Tmp-/Rtmpdm9kpV/downloaded_packages? >> library(flowcore) > Error in library(flowcore) : there is no package called 'flowcore' > In addition: Warning message: > In install.packages(c("flowCore"), lib = > "/Library/Frameworks/R.framework/Resources/library/", ?: > ?installation of package 'flowCore' had non-zero exit status >> > > ? ? ? ?[[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >

ADD COMMENT • link 14.7 years ago Sean Davis 21k

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Benilton Carvalho ★ 4.3k

@benilton-carvalho-1375

Last seen 4.7 years ago

Brazil/Campinas/UNICAMP

Although you didn't tell us, it seems you're running Mac OS X... Because you're trying to install from the source, you need to install XCode (it is on your Mac OS X DVD). I wonder why the binaries were not sufficient for you... source("http://www.bioconductor.org/biocLite.R") biocLite("flowCore") should get you going just fine (and you wouldn't need to install XCode) b On Tue, Mar 16, 2010 at 4:40 PM, Abbhirami Rajagopal <abbhirami at="" gmail.com=""> wrote: > Hi > > I am new to R and bioconductor, I have been trying to download the packages > for flow cytometry data analysis > > Below is the error message I got- I had to reinstall R a few times before I > got to this stage. The installation seemed to have work fine but I still > cannot get the package- please HELP > > Regds > Abi > > * installing *source* package ?flowCore? ... > ** libs > ** arch - i386 > sh: make: command not found > ERROR: compilation failed for package ?flowCore? > * removing > ?/Library/Frameworks/R.framework/Versions/2.10/Resources/library/flo wCore? > * restoring previous > ?/Library/Frameworks/R.framework/Versions/2.10/Resources/library/flo wCore? > > The downloaded packages are in > ?/private/var/folders/32/32m0GhxDHKS- TBOPVk6WIU+++TI/-Tmp-/Rtmpdm9kpV/downloaded_packages? >> library(flowcore) > Error in library(flowcore) : there is no package called 'flowcore' > In addition: Warning message: > In install.packages(c("flowCore"), lib = > "/Library/Frameworks/R.framework/Resources/library/", ?: > ?installation of package 'flowCore' had non-zero exit status >> > > ? ? ? ?[[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >

ADD COMMENT • link 14.7 years ago Benilton Carvalho ★ 4.3k

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Thank you all- I installed XCode and I was able to download the package. Regds Abi On Tue, Mar 16, 2010 at 12:52 PM, Benilton Carvalho < beniltoncarvalho@gmail.com> wrote: > Although you didn't tell us, it seems you're running Mac OS X... > > Because you're trying to install from the source, you need to install > XCode (it is on your Mac OS X DVD). > > I wonder why the binaries were not sufficient for you... > > source("http://www.bioconductor.org/biocLite.R") > biocLite("flowCore") > > should get you going just fine (and you wouldn't need to install XCode) > > b > > On Tue, Mar 16, 2010 at 4:40 PM, Abbhirami Rajagopal > <abbhirami@gmail.com> wrote: > > Hi > > > > I am new to R and bioconductor, I have been trying to download the > packages > > for flow cytometry data analysis > > > > Below is the error message I got- I had to reinstall R a few times before > I > > got to this stage. The installation seemed to have work fine but I still > > cannot get the package- please HELP > > > > Regds > > Abi > > > > * installing *source* package flowCore ... > > ** libs > > ** arch - i386 > > sh: make: command not found > > ERROR: compilation failed for package flowCore > > * removing > > > /Library/Frameworks/R.framework/Versions/2.10/Resources/library/flo wCore > > * restoring previous > > > /Library/Frameworks/R.framework/Versions/2.10/Resources/library/flo wCore > > > > The downloaded packages are in > > > /private/var/folders/32/32m0GhxDHKS- TBOPVk6WIU+++TI/-Tmp-/Rtmpdm9kpV/downloaded_packages > >> library(flowcore) > > Error in library(flowcore) : there is no package called 'flowcore' > > In addition: Warning message: > > In install.packages(c("flowCore"), lib = > > "/Library/Frameworks/R.framework/Resources/library/", : > > installation of package 'flowCore' had non-zero exit status > >> > > > > [[alternative HTML version deleted]] > > > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > [[alternative HTML version deleted]]

ADD REPLY • link 14.7 years ago Abbhirami Rajagopal ▴ 70

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