Question: About KEGGgraph supplementary information
0
gravatar for Jitao Zhang
8.9 years ago by
Jitao Zhang20
Jitao Zhang20 wrote:
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi dear Alper, I don't know this problem before and it seems to me rather that this is caused by the Rgraphviz library. Could you please try > library(Rgraphviz) If it prints the same error codes, please follow the suggestions it gives (for example to change PATH variable). If the problem still exists, please feel free to write to bioconductor mail-list (I have cc-ed there). People in the Rgraphviz group will definitely like to help. Best wishes, David Uzun, Alper wrote: > Hi David, > > Thank you very much for your swift response. > > Actually I need to ask one more question, when I try to load the library (> library(KEGGgraph) ) > It gives an error. By the way I already installed Graphviz program. I guess It cant find the the program > what is your suggestion to solve it? > > Error is pasted below; > Thank you > Alper > ************************************************************** >> library(KEGGgraph) > Loading required package: XML > Loading required package: graph > > Attaching package: 'graph' > > The following object(s) are masked from 'package:XML': > > addNode > > Loading required package: Rgraphviz > Loading required package: grid > Error : .onLoad failed in loadNamespace() for 'Rgraphviz', details: > call: value[[3L]](cond) > error: unable to load shared object 'C:/PROGRA~1/R/R-212~1.0/library/Rgraphviz/libs/i386/Rgraphviz.dll': > LoadLibrary failure: The specified module could not be found. > > Check that (1) graphviz is installed on your system; (2) the > installed version of graphviz matches '2.20.3'; this is the version > used to build this Rgraphviz package; (3) graphviz is accessible to > R, e.g., the path to the graphviz 'bin' directory is in the system > 'PATH' variable. See additional instructions in the 'README' file of > the Rgraphviz 'source' distribution, available at > > ************************************************************** > > > > > > -----Original Message----- > From: Jitao Zhang [mailto:j.zhang at dkfz-heidelberg.de] > Sent: Wednesday, November 10, 2010 4:26 AM > To: Uzun, Alper > Subject: Re: About KEGGgraph supplementary information > > Hi dear Alper, > > Thanks for your notification. The file is attached. It was for the version published in 2008 and since then some codes had to be changed due to the KEGG upgrade. Please turn to the KEGGgraph documentation for any questions and don't hesitate to contact me in case further questions exist. > > Best wishes, > David > > Uzun, Alper wrote: >> Dear Dr. Zhang, > >> I was reading your article and try to reach supplementary information at Bioinformatics Journal, but unfortunately it is not reachable (The link says "not found"). >> Could you please send me this supplementary information at your convenience? > >> Thank you >> Alper > >> ------------------------------------------------------------------- >> Alper Uzun, Ph.D. >> Women & Infants Hospital, Department of Pediatrics. >> Brown University, Center for Computational Molecular Biology. >> Alpert Medical School, Bio-Med Pediatrics. >> Providence, RI, USA >> ------------------------------------------------------------------- >> http://www.womenandinfants.org/<blocked::http: www.womenandinfants.or="">> g/> http://www.brown.edu/<blocked::http: www.brown.edu=""/> > > >> ________________________________ >> This e-mail and any files transmitted with it are confidential and >> intended solely for the use of the individual or entity to whom they >> are addressed. If you are not the intended recipient, you are hereby >> notified that any disclosure, copying, distribution or taking of any >> action in reliance on the information contained in this e-mail is prohibited. If you have received this e-mail in error, please notify sender by reply e-mail and delete this message and any attachment(s) immediately. Thank you for your consideration in this matter. > > > This e-mail and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution or taking of any action in reliance on the information contained in this e-mail is prohibited. If you have received this e-mail in error, please notify sender by reply e-mail and delete this message and any attachment(s) immediately. Thank you for your consideration in this matter. - -- PLEASE BE GREEN, THINK BEFORE YOU PRINT Jitao David Zhang Computational Biology/Biostatistics Ph.D. Candidate Division of Molecular Genome Analysis, DKFZ Im Neuenheimer Feld 580, Heidelberg D-69120 Germany Tel: 49-(0)6221-423458 Calendar: http://www.google.com/calendar/embed?src=38m77vcknecr59sbpdj0vofndo%40 group.calendar.google.com -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.9 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iEYEARECAAYFAkzbpsIACgkQb+FFFSdYGiANSgCfVQ0G+0pJODgO3p2nFHbuVxC5 F4IAnj6cDyDsKZG8PiZqlaB/d9yUHgAY =cHQN -----END PGP SIGNATURE-----
rgraphviz kegggraph • 570 views
ADD COMMENTlink modified 8.9 years ago by Uzun, Alper10 • written 8.9 years ago by Jitao Zhang20
Answer: About KEGGgraph supplementary information
0
gravatar for Uzun, Alper
8.9 years ago by
Uzun, Alper10
Uzun, Alper10 wrote:
Hi David, Yes it creates the same error, okay I will post this error, If I can't fix it soon. It seems like original Graphviz and R don't see each other, and I agree with your suggestion it may be about PATH description. Thank you Alper -----Original Message----- From: Jitao Zhang [mailto:j.zhang@dkfz-heidelberg.de] Sent: Thursday, November 11, 2010 3:18 AM To: Uzun, Alper Cc: bioconductor at stat.math.ethz.ch Subject: Re: About KEGGgraph supplementary information -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi dear Alper, I don't know this problem before and it seems to me rather that this is caused by the Rgraphviz library. Could you please try > library(Rgraphviz) If it prints the same error codes, please follow the suggestions it gives (for example to change PATH variable). If the problem still exists, please feel free to write to bioconductor mail-list (I have cc-ed there). People in the Rgraphviz group will definitely like to help. Best wishes, David Uzun, Alper wrote: > Hi David, > > Thank you very much for your swift response. > > Actually I need to ask one more question, when I try to load the library (> library(KEGGgraph) ) > It gives an error. By the way I already installed Graphviz program. I guess It cant find the the program > what is your suggestion to solve it? > > Error is pasted below; > Thank you > Alper > ************************************************************** >> library(KEGGgraph) > Loading required package: XML > Loading required package: graph > > Attaching package: 'graph' > > The following object(s) are masked from 'package:XML': > > addNode > > Loading required package: Rgraphviz > Loading required package: grid > Error : .onLoad failed in loadNamespace() for 'Rgraphviz', details: > call: value[[3L]](cond) > error: unable to load shared object 'C:/PROGRA~1/R/R-212~1.0/library/Rgraphviz/libs/i386/Rgraphviz.dll': > LoadLibrary failure: The specified module could not be found. > > Check that (1) graphviz is installed on your system; (2) the > installed version of graphviz matches '2.20.3'; this is the version > used to build this Rgraphviz package; (3) graphviz is accessible to > R, e.g., the path to the graphviz 'bin' directory is in the system > 'PATH' variable. See additional instructions in the 'README' file of > the Rgraphviz 'source' distribution, available at > > ************************************************************** > > > > > > -----Original Message----- > From: Jitao Zhang [mailto:j.zhang at dkfz-heidelberg.de] > Sent: Wednesday, November 10, 2010 4:26 AM > To: Uzun, Alper > Subject: Re: About KEGGgraph supplementary information > > Hi dear Alper, > > Thanks for your notification. The file is attached. It was for the version published in 2008 and since then some codes had to be changed due to the KEGG upgrade. Please turn to the KEGGgraph documentation for any questions and don't hesitate to contact me in case further questions exist. > > Best wishes, > David > > Uzun, Alper wrote: >> Dear Dr. Zhang, > >> I was reading your article and try to reach supplementary information at Bioinformatics Journal, but unfortunately it is not reachable (The link says "not found"). >> Could you please send me this supplementary information at your convenience? > >> Thank you >> Alper > >> ------------------------------------------------------------------- >> Alper Uzun, Ph.D. >> Women & Infants Hospital, Department of Pediatrics. >> Brown University, Center for Computational Molecular Biology. >> Alpert Medical School, Bio-Med Pediatrics. >> Providence, RI, USA >> ------------------------------------------------------------------- >> http://www.womenandinfants.org/<blocked::http: www.womenandinfants.or="">> g/> http://www.brown.edu/<blocked::http: www.brown.edu=""/> > > >> ________________________________ >> This e-mail and any files transmitted with it are confidential and >> intended solely for the use of the individual or entity to whom they >> are addressed. If you are not the intended recipient, you are hereby >> notified that any disclosure, copying, distribution or taking of any >> action in reliance on the information contained in this e-mail is prohibited. If you have received this e-mail in error, please notify sender by reply e-mail and delete this message and any attachment(s) immediately. Thank you for your consideration in this matter. > > > This e-mail and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution or taking of any action in reliance on the information contained in this e-mail is prohibited. If you have received this e-mail in error, please notify sender by reply e-mail and delete this message and any attachment(s) immediately. Thank you for your consideration in this matter. - -- PLEASE BE GREEN, THINK BEFORE YOU PRINT Jitao David Zhang Computational Biology/Biostatistics Ph.D. Candidate Division of Molecular Genome Analysis, DKFZ Im Neuenheimer Feld 580, Heidelberg D-69120 Germany Tel: 49-(0)6221-423458 Calendar: http://www.google.com/calendar/embed?src=38m77vcknecr59sbpdj0vofndo%40 group.calendar.google.com -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.9 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iEYEARECAAYFAkzbpsIACgkQb+FFFSdYGiANSgCfVQ0G+0pJODgO3p2nFHbuVxC5 F4IAnj6cDyDsKZG8PiZqlaB/d9yUHgAY =cHQN -----END PGP SIGNATURE----- This e-mail and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution or taking of any action in reliance on the information contained in this e-mail is prohibited. If you have received this e-mail in error, please notify sender by reply e-mail and delete this message and any attachment(s) immediately. Thank you for your consideration in this matter.
ADD COMMENTlink written 8.9 years ago by Uzun, Alper10
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