I think this hunch is off the mark... the file name is fine as it is... if anything will confuse R it would be that the data inside the file are not what was expected. If in fact the file is csv formatted then the function to read it would be read.csv [1] or read.table [2]. Read the help pages for these functions and read the R Data Import/Export documentation [3]. [1] ?read.csv at R console [2] ?read.table many of the options for this function will work for read.csv. [3] https://cran.r-project.org/doc/manuals/r-release/R-data.html On August 19, 2018 12:16:14 PM PDT, "Sparks, John" <jspark4 at uic.edu> wrote:>Just a hunch, but I would recommend simplifying your filename: remove >the (CSV) portion. It could be confusing in R read syntax. Create a >filename with no unnecessary punctuation and no blank spaces. > > >--John Sparks > > >________________________________ >From: R-help <r-help-bounces at r-project.org> on behalf of Spencer >Brackett <spbrackett20 at saintjosephhs.com> >Sent: Sunday, August 19, 2018 2:11 PM >To: r-help at r-project.org >Subject: [R] Request for R Assistance: Downloading Data > >Good evening, > >I am attempting to download Genomic data from the GDC onto R for >analysis >and am experiencing some difficulty. I have downloaded the GDC data >into an >Excel, CSV, and notepad (.txt) file and implemented what I believe to >be >the proper arguments, with every attempting failing to properly load >the >data onto R. The following is the various attempts I made in trying to >take >one of these files (a translated version of the GDC data) and load it >into R >. > >> load("C:\\Users\\Spencer\\Desktop\\LGG Drug (CSV).csv") >Error in load("C:\\Users\\Spencer\\Desktop\\LGG Drug (CSV).csv") : >bad restore file magic number (file may be corrupted) -- no data loaded >In addition: Warning message: >file ?LGG Drug (CSV).csv? has magic number 'MANIF' > Use of save versions prior to 2 is deprecated >> LGG Drug<-read.table("C:\\Users\\Spencer\\Desktop\\LGG Drug >(CSV).csv",header=TRUE,sep=",") >Error: unexpected symbol in "LGG Drug" >> LGG Drug<-read.table("C: >Error: unexpected symbol in "LGG Drug" >> load("C:\\Users\\Spencer\\Desktop\\DRUG TRIAL GBM.txt") >Error in load("C:\\Users\\Spencer\\Desktop\\DRUG TRIAL GBM.txt") : >bad restore file magic number (file may be corrupted) -- no data loaded >In addition: Warning message: >file ?DRUG TRIAL GBM.txt? has magic number 'MANIF' > Use of save versions prior to 2 is deprecated >> GBM Drug<-read.table("C:\\Users\\Spencer\\Desktop\\DRUG TRIAL >GBM.txt",header=TRUE,sep="") >Error: unexpected symbol in "GBM Drug" >> GBM Drug<-read.table("C:\\Users\\Spencer\\Desktop\\DRUG TRIAL >GBM.txt",header=TRUE,sep="\t") >Error: unexpected symbol in "GBM Drug" >> GBM Drug<-read.table("C:\\Users\\Spencer\\Desktop\\DRUG TRIAL >GBM.txt",header=TRUE,sep="") >Error: unexpected symbol in "GBM Drug" >> GBM Drug<-read.table("C:\\Users\\Spencer\\Desktop\\DRUG TRIAL >GBM.txt",header=TRUE,sep="\t") >Error: unexpected symbol in " GBM Drug" >> load("C:\\Users\\Spencer\\Desktop\\DRUG TRIAL GBM(word wrap).txt") >Error in load("C:\\Users\\Spencer\\Desktop\\DRUG TRIAL GBM(word >wrap).txt") >: >bad restore file magic number (file may be corrupted) -- no data loaded >In addition: Warning message: >file ?DRUG TRIAL GBM(word wrap).txt? has magic number 'MANIF' > Use of save versions prior to 2 is deprecated >> GBM Drug<-read.table("C:\\Users\\Spencer\\Desktop\\DRUG TRIAL >GBM(word >wrap).txt",header=TRUE,sep="") >Error: unexpected symbol in "GBM Drug" > >Any insight into what perhaps I am inputting that is causes this >reoccurring error? Any suggestions as to another procedure for moving >forward would be greatly appreciated! > >Many thanks, > >Spencer Brackett > > [[alternative HTML version deleted]] > >______________________________________________ >R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see >https://stat.ethz.ch/mailman/listinfo/r-help >R-help -- Main R Mailing List: Primary help - Homepage - >SfS<https://stat.ethz.ch/mailman/listinfo/r-help> >stat.ethz.ch >The main R mailing list, for announcements about the development of R >and the availability of new code, questions and answers about problems >and solutions using R, enhancements and patches to the source code and >documentation of R, comparison and compatibility with S and S-plus, and >for the posting of nice examples and benchmarks. > > > >PLEASE do read the posting guide >http://www.R-project.org/posting-guide.html >and provide commented, minimal, self-contained, reproducible code. > > [[alternative HTML version deleted]]-- Sent from my phone. Please excuse my brevity.
I agree with Jeff. The data type is the problem. I wrote what I wrote without looking at the problem very carefully. --JJS ________________________________ From: Jeff Newmiller <jdnewmil at dcn.davis.ca.us> Sent: Sunday, August 19, 2018 4:38 PM To: r-help at r-project.org; Sparks, John; Spencer Brackett; r-help at r-project.org Subject: Re: [R] Request for R Assistance: Downloading Data I think this hunch is off the mark... the file name is fine as it is... if anything will confuse R it would be that the data inside the file are not what was expected. If in fact the file is csv formatted then the function to read it would be read.csv [1] or read.table [2]. Read the help pages for these functions and read the R Data Import/Export documentation [3]. [1] ?read.csv at R console [2] ?read.table many of the options for this function will work for read.csv. [3] https://cran.r-project.org/doc/manuals/r-release/R-data.html R Data Import/Export<https://cran.r-project.org/doc/manuals/r-release/R-data.html> cran.r-project.org 1.1 Imports. The easiest form of data to import into R is a simple text file, and this will often be acceptable for problems of small or medium scale. On August 19, 2018 12:16:14 PM PDT, "Sparks, John" <jspark4 at uic.edu> wrote:>Just a hunch, but I would recommend simplifying your filename: remove >the (CSV) portion. It could be confusing in R read syntax. Create a >filename with no unnecessary punctuation and no blank spaces. > > >--John Sparks > > >________________________________ >From: R-help <r-help-bounces at r-project.org> on behalf of Spencer >Brackett <spbrackett20 at saintjosephhs.com> >Sent: Sunday, August 19, 2018 2:11 PM >To: r-help at r-project.org >Subject: [R] Request for R Assistance: Downloading Data > >Good evening, > >I am attempting to download Genomic data from the GDC onto R for >analysis >and am experiencing some difficulty. I have downloaded the GDC data >into an >Excel, CSV, and notepad (.txt) file and implemented what I believe to >be >the proper arguments, with every attempting failing to properly load >the >data onto R. The following is the various attempts I made in trying to >take >one of these files (a translated version of the GDC data) and load it >into R >. > >> load("C:\\Users\\Spencer\\Desktop\\LGG Drug (CSV).csv") >Error in load("C:\\Users\\Spencer\\Desktop\\LGG Drug (CSV).csv") : >bad restore file magic number (file may be corrupted) -- no data loaded >In addition: Warning message: >file ?LGG Drug (CSV).csv? has magic number 'MANIF' > Use of save versions prior to 2 is deprecated >> LGG Drug<-read.table("C:\\Users\\Spencer\\Desktop\\LGG Drug >(CSV).csv",header=TRUE,sep=",") >Error: unexpected symbol in "LGG Drug" >> LGG Drug<-read.table("C: >Error: unexpected symbol in "LGG Drug" >> load("C:\\Users\\Spencer\\Desktop\\DRUG TRIAL GBM.txt") >Error in load("C:\\Users\\Spencer\\Desktop\\DRUG TRIAL GBM.txt") : >bad restore file magic number (file may be corrupted) -- no data loaded >In addition: Warning message: >file ?DRUG TRIAL GBM.txt? has magic number 'MANIF' > Use of save versions prior to 2 is deprecated >> GBM Drug<-read.table("C:\\Users\\Spencer\\Desktop\\DRUG TRIAL >GBM.txt",header=TRUE,sep="") >Error: unexpected symbol in "GBM Drug" >> GBM Drug<-read.table("C:\\Users\\Spencer\\Desktop\\DRUG TRIAL >GBM.txt",header=TRUE,sep="\t") >Error: unexpected symbol in "GBM Drug" >> GBM Drug<-read.table("C:\\Users\\Spencer\\Desktop\\DRUG TRIAL >GBM.txt",header=TRUE,sep="") >Error: unexpected symbol in "GBM Drug" >> GBM Drug<-read.table("C:\\Users\\Spencer\\Desktop\\DRUG TRIAL >GBM.txt",header=TRUE,sep="\t") >Error: unexpected symbol in " GBM Drug" >> load("C:\\Users\\Spencer\\Desktop\\DRUG TRIAL GBM(word wrap).txt") >Error in load("C:\\Users\\Spencer\\Desktop\\DRUG TRIAL GBM(word >wrap).txt") >: >bad restore file magic number (file may be corrupted) -- no data loaded >In addition: Warning message: >file ?DRUG TRIAL GBM(word wrap).txt? has magic number 'MANIF' > Use of save versions prior to 2 is deprecated >> GBM Drug<-read.table("C:\\Users\\Spencer\\Desktop\\DRUG TRIAL >GBM(word >wrap).txt",header=TRUE,sep="") >Error: unexpected symbol in "GBM Drug" > >Any insight into what perhaps I am inputting that is causes this >reoccurring error? Any suggestions as to another procedure for moving >forward would be greatly appreciated! > >Many thanks, > >Spencer Brackett > > [[alternative HTML version deleted]] > >______________________________________________ >R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see >https://stat.ethz.ch/mailman/listinfo/r-help >R-help -- Main R Mailing List: Primary help - Homepage - >SfS<https://stat.ethz.ch/mailman/listinfo/r-help> >stat.ethz.ch >The main R mailing list, for announcements about the development of R >and the availability of new code, questions and answers about problems >and solutions using R, enhancements and patches to the source code and >documentation of R, comparison and compatibility with S and S-plus, and >for the posting of nice examples and benchmarks. > > > >PLEASE do read the posting guide >http://www.R-project.org/posting-guide.html >and provide commented, minimal, self-contained, reproducible code. > > [[alternative HTML version deleted]]-- Sent from my phone. Please excuse my brevity. [[alternative HTML version deleted]]
Please ignore my last post/inquiry... I have solved the problem. Thanks again for the help! On Sun, Aug 19, 2018 at 5:43 PM Sparks, John <jspark4 at uic.edu> wrote:> I agree with Jeff. The data type is the problem. I wrote what I wrote > without looking at the problem very carefully. > > > --JJS > > > ------------------------------ > *From:* Jeff Newmiller <jdnewmil at dcn.davis.ca.us> > *Sent:* Sunday, August 19, 2018 4:38 PM > *To:* r-help at r-project.org; Sparks, John; Spencer Brackett; > r-help at r-project.org > *Subject:* Re: [R] Request for R Assistance: Downloading Data > > I think this hunch is off the mark... the file name is fine as it is... if > anything will confuse R it would be that the data inside the file are not > what was expected. > > If in fact the file is csv formatted then the function to read it would be > read.csv [1] or read.table [2]. Read the help pages for these functions and > read the R Data Import/Export documentation [3]. > > [1] ?read.csv at R console > [2] ?read.table many of the options for this function will work for > read.csv. > [3] https://cran.r-project.org/doc/manuals/r-release/R-data.html > R Data Import/Export > <https://cran.r-project.org/doc/manuals/r-release/R-data.html> > cran.r-project.org > 1.1 Imports. The easiest form of data to import into R is a simple text > file, and this will often be acceptable for problems of small or medium > scale. > > > > On August 19, 2018 12:16:14 PM PDT, "Sparks, John" <jspark4 at uic.edu> > wrote: > >Just a hunch, but I would recommend simplifying your filename: remove > >the (CSV) portion. It could be confusing in R read syntax. Create a > >filename with no unnecessary punctuation and no blank spaces. > > > > > >--John Sparks > > > > > >________________________________ > >From: R-help <r-help-bounces at r-project.org> on behalf of Spencer > >Brackett <spbrackett20 at saintjosephhs.com> > >Sent: Sunday, August 19, 2018 2:11 PM > >To: r-help at r-project.org > >Subject: [R] Request for R Assistance: Downloading Data > > > >Good evening, > > > >I am attempting to download Genomic data from the GDC onto R for > >analysis > >and am experiencing some difficulty. I have downloaded the GDC data > >into an > >Excel, CSV, and notepad (.txt) file and implemented what I believe to > >be > >the proper arguments, with every attempting failing to properly load > >the > >data onto R. The following is the various attempts I made in trying to > >take > >one of these files (a translated version of the GDC data) and load it > >into R > >. > > > >> load("C:\\Users\\Spencer\\Desktop\\LGG Drug (CSV).csv") > >Error in load("C:\\Users\\Spencer\\Desktop\\LGG Drug (CSV).csv") : > >bad restore file magic number (file may be corrupted) -- no data loaded > >In addition: Warning message: > >file ?LGG Drug (CSV).csv? has magic number 'MANIF' > > Use of save versions prior to 2 is deprecated > >> LGG Drug<-read.table("C:\\Users\\Spencer\\Desktop\\LGG Drug > >(CSV).csv",header=TRUE,sep=",") > >Error: unexpected symbol in "LGG Drug" > >> LGG Drug<-read.table("C: > >Error: unexpected symbol in "LGG Drug" > >> load("C:\\Users\\Spencer\\Desktop\\DRUG TRIAL GBM.txt") > >Error in load("C:\\Users\\Spencer\\Desktop\\DRUG TRIAL GBM.txt") : > >bad restore file magic number (file may be corrupted) -- no data loaded > >In addition: Warning message: > >file ?DRUG TRIAL GBM.txt? has magic number 'MANIF' > > Use of save versions prior to 2 is deprecated > >> GBM Drug<-read.table("C:\\Users\\Spencer\\Desktop\\DRUG TRIAL > >GBM.txt",header=TRUE,sep="") > >Error: unexpected symbol in "GBM Drug" > >> GBM Drug<-read.table("C:\\Users\\Spencer\\Desktop\\DRUG TRIAL > >GBM.txt",header=TRUE,sep="\t") > >Error: unexpected symbol in "GBM Drug" > >> GBM Drug<-read.table("C:\\Users\\Spencer\\Desktop\\DRUG TRIAL > >GBM.txt",header=TRUE,sep="") > >Error: unexpected symbol in "GBM Drug" > >> GBM Drug<-read.table("C:\\Users\\Spencer\\Desktop\\DRUG TRIAL > >GBM.txt",header=TRUE,sep="\t") > >Error: unexpected symbol in " GBM Drug" > >> load("C:\\Users\\Spencer\\Desktop\\DRUG TRIAL GBM(word wrap).txt") > >Error in load("C:\\Users\\Spencer\\Desktop\\DRUG TRIAL GBM(word > >wrap).txt") > >: > >bad restore file magic number (file may be corrupted) -- no data loaded > >In addition: Warning message: > >file ?DRUG TRIAL GBM(word wrap).txt? has magic number 'MANIF' > > Use of save versions prior to 2 is deprecated > >> GBM Drug<-read.table("C:\\Users\\Spencer\\Desktop\\DRUG TRIAL > >GBM(word > >wrap).txt",header=TRUE,sep="") > >Error: unexpected symbol in "GBM Drug" > > > >Any insight into what perhaps I am inputting that is causes this > >reoccurring error? Any suggestions as to another procedure for moving > >forward would be greatly appreciated! > > > >Many thanks, > > > >Spencer Brackett > > > > [[alternative HTML version deleted]] > > > >______________________________________________ > >R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > >https://stat.ethz.ch/mailman/listinfo/r-help > >R-help -- Main R Mailing List: Primary help - Homepage - > >SfS<https://stat.ethz.ch/mailman/listinfo/r-help> > >stat.ethz.ch > >The main R mailing list, for announcements about the development of R > >and the availability of new code, questions and answers about problems > >and solutions using R, enhancements and patches to the source code and > >documentation of R, comparison and compatibility with S and S-plus, and > >for the posting of nice examples and benchmarks. > > > > > > > >PLEASE do read the posting guide > >http://www.R-project.org/posting-guide.html > >and provide commented, minimal, self-contained, reproducible code. > > > > [[alternative HTML version deleted]] > > -- > Sent from my phone. Please excuse my brevity. >[[alternative HTML version deleted]]