hi to you both You are right peter, I probably miss understood the system.file function. I was trying to use it with a package from bioconductor and when i saw that it didn't work for me, I tested with readxl and still do not working, so I am doing something wrong with system.file the original script was library(SICtools) bam1 <- system.file(package='SICtools','extdata','example1.bam') the example1.bam file is supposed to be at the working directory (i changed the directory using setwd()), it was changed to /home/paumarc/Bam i tried to change extdata for my working directory but it did not work thanks Pau Marc Mu?oz Torres skype: pau_marc http://www.linkedin.com/in/paumarc http://www.researchgate.net/profile/Pau_Marc_Torres3/info/ 2017-05-22 14:53 GMT+02:00 peter dalgaard <pdalgd at gmail.com>:> > > On 22 May 2017, at 14:43 , Pau Marc Mu?oz Torres <paumarc at gmail.com> > wrote: > > > > Hello everybody > > > > I am trying to use system.file but it returns not file found > > > > what I have done is > > > >> sample <- system.file("results.xlsx","estdata", package > > "readxl",mustWork = TRUE) > > Error in system.file("results.xlsx", "estdata", package = "readxl", > > mustWork = TRUE) : > > no file found > > > > i have checked the path was correct and the file exists with > > > > FILES <- file.path("results.xlsx") > > present <- file.exists(FILES) > > > > and it returned a true values. Anyone can tell me which can be the > problem ? > > Not if you don't tell us WHERE you expect to find the file... > > Where is it located, and what is the value of FILES above? > > It is not unlikely that you misunderstande what system.file() is supposed > to do. > > -pd > > > > > > thanks > > > > Pau Marc Mu?oz Torres > > skype: pau_marc > > http://www.linkedin.com/in/paumarc > > http://www.researchgate.net/profile/Pau_Marc_Torres3/info/ > > > > [[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 > > PLEASE do read the posting guide http://www.R-project.org/ > posting-guide.html > > and provide commented, minimal, self-contained, reproducible code. > > -- > Peter Dalgaard, Professor, > Center for Statistics, Copenhagen Business School > Solbjerg Plads 3, 2000 Frederiksberg, Denmark > Phone: (+45)38153501 > Office: A 4.23 > Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com > > > > > > > > > >[[alternative HTML version deleted]]
i could make it worl, thanks for your help, it was usefull Pau Marc Mu?oz Torres skype: pau_marc http://www.linkedin.com/in/paumarc http://www.researchgate.net/profile/Pau_Marc_Torres3/info/ 2017-05-22 15:38 GMT+02:00 Pau Marc Mu?oz Torres <paumarc at gmail.com>:> hi to you both > > You are right peter, I probably miss understood the system.file function. > I was trying to use it with a package from bioconductor and when i saw that > it didn't work for me, I tested with readxl and still do not working, so I > am doing something wrong with system.file > > the original script was > > > library(SICtools) > > bam1 <- system.file(package='SICtools','extdata','example1.bam') > > the example1.bam file is supposed to be at the working directory (i > changed the directory using setwd()), it was changed to /home/paumarc/Bam > > i tried to change extdata for my working directory but it did not work > > thanks > > Pau Marc Mu?oz Torres > skype: pau_marc > http://www.linkedin.com/in/paumarc > http://www.researchgate.net/profile/Pau_Marc_Torres3/info/ > > > 2017-05-22 14:53 GMT+02:00 peter dalgaard <pdalgd at gmail.com>: > >> >> > On 22 May 2017, at 14:43 , Pau Marc Mu?oz Torres <paumarc at gmail.com> >> wrote: >> > >> > Hello everybody >> > >> > I am trying to use system.file but it returns not file found >> > >> > what I have done is >> > >> >> sample <- system.file("results.xlsx","estdata", package >> > "readxl",mustWork = TRUE) >> > Error in system.file("results.xlsx", "estdata", package = "readxl", >> > mustWork = TRUE) : >> > no file found >> > >> > i have checked the path was correct and the file exists with >> > >> > FILES <- file.path("results.xlsx") >> > present <- file.exists(FILES) >> > >> > and it returned a true values. Anyone can tell me which can be the >> problem ? >> >> Not if you don't tell us WHERE you expect to find the file... >> >> Where is it located, and what is the value of FILES above? >> >> It is not unlikely that you misunderstande what system.file() is supposed >> to do. >> >> -pd >> >> >> > >> > thanks >> > >> > Pau Marc Mu?oz Torres >> > skype: pau_marc >> > http://www.linkedin.com/in/paumarc >> > http://www.researchgate.net/profile/Pau_Marc_Torres3/info/ >> > >> > [[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 >> > PLEASE do read the posting guide http://www.R-project.org/posti >> ng-guide.html >> > and provide commented, minimal, self-contained, reproducible code. >> >> -- >> Peter Dalgaard, Professor, >> Center for Statistics, Copenhagen Business School >> Solbjerg Plads 3, 2000 Frederiksberg, Denmark >> Phone: (+45)38153501 >> Office: A 4.23 >> Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com >> >> >> >> >> >> >> >> >> >> >[[alternative HTML version deleted]]
Windows. A funny name for a operating system that doesn't let you see anything. Jim On Mon, May 22, 2017 at 11:59 PM, Pau Marc Mu?oz Torres <paumarc at gmail.com> wrote:> i could make it worl, thanks for your help, it was usefull > > Pau Marc Mu?oz Torres > skype: pau_marc > http://www.linkedin.com/in/paumarc > http://www.researchgate.net/profile/Pau_Marc_Torres3/info/ > > > 2017-05-22 15:38 GMT+02:00 Pau Marc Mu?oz Torres <paumarc at gmail.com>: > >> hi to you both >> >> You are right peter, I probably miss understood the system.file function. >> I was trying to use it with a package from bioconductor and when i saw that >> it didn't work for me, I tested with readxl and still do not working, so I >> am doing something wrong with system.file >> >> the original script was >> >> >> library(SICtools) >> >> bam1 <- system.file(package='SICtools','extdata','example1.bam') >> >> the example1.bam file is supposed to be at the working directory (i >> changed the directory using setwd()), it was changed to /home/paumarc/Bam >> >> i tried to change extdata for my working directory but it did not work >> >> thanks >> >> Pau Marc Mu?oz Torres >> skype: pau_marc >> http://www.linkedin.com/in/paumarc >> http://www.researchgate.net/profile/Pau_Marc_Torres3/info/ >> >> >> 2017-05-22 14:53 GMT+02:00 peter dalgaard <pdalgd at gmail.com>: >> >>> >>> > On 22 May 2017, at 14:43 , Pau Marc Mu?oz Torres <paumarc at gmail.com> >>> wrote: >>> > >>> > Hello everybody >>> > >>> > I am trying to use system.file but it returns not file found >>> > >>> > what I have done is >>> > >>> >> sample <- system.file("results.xlsx","estdata", package >>> > "readxl",mustWork = TRUE) >>> > Error in system.file("results.xlsx", "estdata", package = "readxl", >>> > mustWork = TRUE) : >>> > no file found >>> > >>> > i have checked the path was correct and the file exists with >>> > >>> > FILES <- file.path("results.xlsx") >>> > present <- file.exists(FILES) >>> > >>> > and it returned a true values. Anyone can tell me which can be the >>> problem ? >>> >>> Not if you don't tell us WHERE you expect to find the file... >>> >>> Where is it located, and what is the value of FILES above? >>> >>> It is not unlikely that you misunderstande what system.file() is supposed >>> to do. >>> >>> -pd >>> >>> >>> > >>> > thanks >>> > >>> > Pau Marc Mu?oz Torres >>> > skype: pau_marc >>> > http://www.linkedin.com/in/paumarc >>> > http://www.researchgate.net/profile/Pau_Marc_Torres3/info/ >>> > >>> > [[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 >>> > PLEASE do read the posting guide http://www.R-project.org/posti >>> ng-guide.html >>> > and provide commented, minimal, self-contained, reproducible code. >>> >>> -- >>> Peter Dalgaard, Professor, >>> Center for Statistics, Copenhagen Business School >>> Solbjerg Plads 3, 2000 Frederiksberg, Denmark >>> Phone: (+45)38153501 >>> Office: A 4.23 >>> Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >> > > [[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 > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.