pckg Resourcerer : can't read "affy_HG-U133_Plus_2.zip" with getResourcerer()
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@guillaume-tiberi-4785
Last seen 7.2 years ago
Hi all I want to load annotation file "affy_HG-U133_Plus_2.zip" with "Resourcerer" and its function getResourcerer(). Sorry for french error_message ;) library("Resourcerer") list.files(file.path(.path.package("Resourcerer"), "temp")) *# > [1] "README"* annot <- getResourcerer( "affy_HG-U133_Plus_2.zip", organism = "human", destDir = file.path(.path.package("Resourcerer"), "temp"), baseUrl = "ftp://occams.dfci.harvard.edu/pub/bio/tgi/data/Resourcerer", clean = TRUE, exten = "zip" ) # *Erreur dans file(file, "rt") : impossible d'ouvrir la connexion* *# De plus : Message d'avis :* *# In file(file, "rt") :* *# impossible d'ouvrir le fichier '/home/tiberi/R/i486-pc-linux-gnu-library/2.10/Resourcerer/temp /affy_HG-U133_Plus_2' : Aucun fichier ou dossier de ce type* ls() *# character(0)* # Files are created list.files(file.path(.path.package("Resourcerer"), "temp")) *# > [1] "affy_U133Plus2" "file643c9869affy_HG-U133_Plus_2.zip" "README"* * * # You can see the problem is uncorrectly named : temp file was named "affy_U133Plus2" instead of "affy_HG-U133Plus2". "HG-" is missing # Strangely, exemple shown in ?getResourcerer() is functionnal, and resourcerer object is correctly created resourcerer <- getResourcerer( "Agilent_Human1_cDNA.zip", organism = "human", destDir = file.path(.path.package("Resourcerer"), "temp"), baseUrl = "ftp://occams.dfci.harvard.edu/pub/bio/tgi/data/Resourcerer", clean = TRUE, exten = "zip" ) > ls() # [1] "resourcerer" Have you got an idear ? thanks Guillaume [[alternative HTML version deleted]]
Annotation Organism Annotation Organism • 898 views
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@freudenberg-johannes-nihniehs-e-4789
Last seen 7.2 years ago
It seems that the function getResourcerer() expects to find a file named "affy_HG-U133_Plus_2" in the destDir after unzipping the file "affy_HG-U133_Plus_2.zip" However, it finds a file named "affy_U133Plus2" instead. I would probably just rename the file accordingly and run the same function call again, e.g. > annot <- getResourcerer("affy_HG-U133_Plus_2.zip", organism = "Human") Error in file(file, "rt") : cannot open the connection In addition: Warning message: In file(file, "rt") : cannot open file '... /Resourcerer/temp/affy_HG-U133_Plus_2': No such file or directory > file.rename(paste(file.path(.path.package("Resourcerer"), "temp"), "affy_U133Plus2", sep="/"), paste(file.path(.path.package("Resourcerer"), "temp"), "affy_HG- U133_Plus_2", sep="/")) [1] TRUE > annot <- getResourcerer("affy_HG-U133_Plus_2.zip", organism = "Human") --Johannes /home/freudenbergjm/R/x86_64-redhat-linux-gnu- library/2.13/Resourcerer/temp/ Browse[1]> fileName <- "/home/freudenbergjm/R/x86_64-redhat-linux-gnu- library/2.13/Resourcerer/temp/affy_U133Plus2" -----Original Message----- From: Guillaume Tiberi [mailto:guillaume.tiberi@gmail.com] Sent: Tuesday, August 02, 2011 11:40 AM To: bioconductor at r-project.org Subject: [BioC] pckg Resourcerer : can't read "affy_HG- U133_Plus_2.zip" with getResourcerer() Hi all I want to load annotation file "affy_HG-U133_Plus_2.zip" with "Resourcerer" and its function getResourcerer(). Sorry for french error_message ;) library("Resourcerer") list.files(file.path(.path.package("Resourcerer"), "temp")) *# > [1] "README"* annot <- getResourcerer( "affy_HG-U133_Plus_2.zip", organism = "human", destDir = file.path(.path.package("Resourcerer"), "temp"), baseUrl = "ftp://occams.dfci.harvard.edu/pub/bio/tgi/data/Resourcerer", clean = TRUE, exten = "zip" ) # *Erreur dans file(file, "rt") : impossible d'ouvrir la connexion* *# De plus : Message d'avis :* *# In file(file, "rt") :* *# impossible d'ouvrir le fichier '/home/tiberi/R/i486-pc-linux-gnu- library/2.10/Resourcerer/temp/affy_HG-U133_Plus_2' : Aucun fichier ou dossier de ce type* ls() *# character(0)* # Files are created list.files(file.path(.path.package("Resourcerer"), "temp")) *# > [1] "affy_U133Plus2" "file643c9869affy_HG-U133_Plus_2.zip" "README"* * * # You can see the problem is uncorrectly named : temp file was named "affy_U133Plus2" instead of "affy_HG-U133Plus2". "HG-" is missing # Strangely, exemple shown in ?getResourcerer() is functionnal, and resourcerer object is correctly created resourcerer <- getResourcerer( "Agilent_Human1_cDNA.zip", organism = "human", destDir = file.path(.path.package("Resourcerer"), "temp"), baseUrl = "ftp://occams.dfci.harvard.edu/pub/bio/tgi/data/Resourcerer", clean = TRUE, exten = "zip" ) > ls() # [1] "resourcerer" Have you got an idear ? thanks Guillaume [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Hi, Guillaume, It seems likely a bug in the package. If you just need the annotation of affy HGU133 plus 2, you can simply install the hug133plus2.db package. See more detail, visit http://bioconductor.org/packages/release/data/annotation/html/hgu133 plus2.db.html Chao-Jen -- Chao-Jen Wong Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Avenue N., M1-B514 PO Box 19024 Seattle, WA 98109 206.667.4485 cwon2 at fhcrc.org ----- Original Message ----- From: "Johannes Freudenberg (NIH/NIEHS) [E]" <johannes.freudenberg@nih.gov> To: "Guillaume Tiberi" <guillaume.tiberi at="" gmail.com="">, bioconductor at r-project.org Sent: Tuesday, August 2, 2011 9:49:27 AM Subject: Re: [BioC] pckg Resourcerer : can't read "affy_HG- U133_Plus_2.zip" with getResourcerer() It seems that the function getResourcerer() expects to find a file named "affy_HG-U133_Plus_2" in the destDir after unzipping the file "affy_HG-U133_Plus_2.zip" However, it finds a file named "affy_U133Plus2" instead. I would probably just rename the file accordingly and run the same function call again, e.g. > annot <- getResourcerer("affy_HG-U133_Plus_2.zip", organism = "Human") Error in file(file, "rt") : cannot open the connection In addition: Warning message: In file(file, "rt") : cannot open file '... /Resourcerer/temp/affy_HG-U133_Plus_2': No such file or directory > file.rename(paste(file.path(.path.package("Resourcerer"), "temp"), "affy_U133Plus2", sep="/"), paste(file.path(.path.package("Resourcerer"), "temp"), "affy_HG- U133_Plus_2", sep="/")) [1] TRUE > annot <- getResourcerer("affy_HG-U133_Plus_2.zip", organism = "Human") --Johannes /home/freudenbergjm/R/x86_64-redhat-linux-gnu- library/2.13/Resourcerer/temp/ Browse[1]> fileName <- "/home/freudenbergjm/R/x86_64-redhat-linux-gnu- library/2.13/Resourcerer/temp/affy_U133Plus2" -----Original Message----- From: Guillaume Tiberi [mailto:guillaume.tiberi@gmail.com] Sent: Tuesday, August 02, 2011 11:40 AM To: bioconductor at r-project.org Subject: [BioC] pckg Resourcerer : can't read "affy_HG- U133_Plus_2.zip" with getResourcerer() Hi all I want to load annotation file "affy_HG-U133_Plus_2.zip" with "Resourcerer" and its function getResourcerer(). Sorry for french error_message ;) library("Resourcerer") list.files(file.path(.path.package("Resourcerer"), "temp")) *# > [1] "README"* annot <- getResourcerer( "affy_HG-U133_Plus_2.zip", organism = "human", destDir = file.path(.path.package("Resourcerer"), "temp"), baseUrl = "ftp://occams.dfci.harvard.edu/pub/bio/tgi/data/Resourcerer", clean = TRUE, exten = "zip" ) # *Erreur dans file(file, "rt") : impossible d'ouvrir la connexion* *# De plus : Message d'avis :* *# In file(file, "rt") :* *# impossible d'ouvrir le fichier '/home/tiberi/R/i486-pc-linux-gnu- library/2.10/Resourcerer/temp/affy_HG-U133_Plus_2' : Aucun fichier ou dossier de ce type* ls() *# character(0)* # Files are created list.files(file.path(.path.package("Resourcerer"), "temp")) *# > [1] "affy_U133Plus2" "file643c9869affy_HG-U133_Plus_2.zip" "README"* * * # You can see the problem is uncorrectly named : temp file was named "affy_U133Plus2" instead of "affy_HG-U133Plus2". "HG-" is missing # Strangely, exemple shown in ?getResourcerer() is functionnal, and resourcerer object is correctly created resourcerer <- getResourcerer( "Agilent_Human1_cDNA.zip", organism = "human", destDir = file.path(.path.package("Resourcerer"), "temp"), baseUrl = "ftp://occams.dfci.harvard.edu/pub/bio/tgi/data/Resourcerer", clean = TRUE, exten = "zip" ) > ls() # [1] "resourcerer" Have you got an idear ? thanks Guillaume [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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