[Bioc-devel] Java version issue on Bioconductor test platform - Bioc-devel

Wed, Sep 2, 2020 1:36 PM #

Hi Arman,

You already asked about this in May:
https://stat.ethz.ch/pipermail/bioc-devel/2020-May/016788.html

Have you followed up with the xlsx maintainers as suggested by Llu?s?

Cheers,
H.

On 8/29/20 11:12, Arman Shahrisa wrote:

_______________________________________________
Bioc-devel at r-project.org mailing list
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=uVvhfQ6BPTCSmaMBY75Fju40h5GVVRhL_eXtphggDFg&s=6pEzMultxNqzC8mdCzk_UKXBj7S18C9lchZUWdKOXlc&e=

Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

Arman Shahrisa

Wed, Sep 2, 2020 11:28 PM #

Hi Herve,

The last response in the previous topic suggested that the maintainer has already fixed the problem on GitHub but not CRAN.

https://stat.ethz.ch/pipermail/bioc-devel/2020-May/016791.html

This is from May and the problem still persists. I?ll try contacting the maintainer of xlsx.

Best regards,
Arman



From: Pages, Herve<mailto:hpages at fredhutch.org>
Sent: Thursday, September 3, 2020 01:06
To: Arman Shahrisa<mailto:shahrisa.arman at hotmail.com>; bioc-devel<mailto:bioc-devel at r-project.org>
Subject: Re: [Bioc-devel] Java version issue on Bioconductor test platform

Hi Arman,

You already asked about this in May:
https://stat.ethz.ch/pipermail/bioc-devel/2020-May/016788.html

Have you followed up with the xlsx maintainers as suggested by Llu?s?

Cheers,
H.

On 8/29/20 11:12, Arman Shahrisa wrote:

_______________________________________________
Bioc-devel at r-project.org mailing list
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=uVvhfQ6BPTCSmaMBY75Fju40h5GVVRhL_eXtphggDFg&s=6pEzMultxNqzC8mdCzk_UKXBj7S18C9lchZUWdKOXlc&e=

--
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

Arman Shahrisa

Wed, Sep 9, 2020 11:06 AM #

Hi to all,

I have sent several emails to the maintainer of ?xlsx? package but unfortunately, he is unresponsive.
Am I allowed to use an alternative package for exporting data only for mac users?

Best regards,
Arman


From: Arman Shahrisa<mailto:shahrisa.arman at hotmail.com>
Sent: Thursday, September 3, 2020 10:59
To: Pages, Herve<mailto:hpages at fredhutch.org>; bioc-devel<mailto:bioc-devel at r-project.org>
Subject: RE: [Bioc-devel] Java version issue on Bioconductor test platform

Hi Herve,

The last response in the previous topic suggested that the maintainer has already fixed the problem on GitHub but not CRAN.

https://stat.ethz.ch/pipermail/bioc-devel/2020-May/016791.html

This is from May and the problem still persists. I?ll try contacting the maintainer of xlsx.

Best regards,
Arman



From: Pages, Herve<mailto:hpages at fredhutch.org>
Sent: Thursday, September 3, 2020 01:06
To: Arman Shahrisa<mailto:shahrisa.arman at hotmail.com>; bioc-devel<mailto:bioc-devel at r-project.org>
Subject: Re: [Bioc-devel] Java version issue on Bioconductor test platform

Hi Arman,

You already asked about this in May:
https://stat.ethz.ch/pipermail/bioc-devel/2020-May/016788.html

Have you followed up with the xlsx maintainers as suggested by Llu?s?

Cheers,
H.

On 8/29/20 11:12, Arman Shahrisa wrote:

_______________________________________________
Bioc-devel at r-project.org mailing list
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=uVvhfQ6BPTCSmaMBY75Fju40h5GVVRhL_eXtphggDFg&s=6pEzMultxNqzC8mdCzk_UKXBj7S18C9lchZUWdKOXlc&e=

--
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

Hervé Pagès

Thu, Sep 10, 2020 10:22 AM #

Hi Arman,

Sure, if xlsx is broken and won't be fixed, use something else. Maybe 
try openxlsx? Similar to xlsx but doesn't require Java:

   https://CRAN.R-project.org/package=openxlsx

But why would you use something else on Mac only? It's easier from a 
maintenance point of view if you use the same code on all platforms, 
whenever possible.

Best,
H.

On 9/9/20 11:06, Arman Shahrisa wrote:

Hi to all,

I have sent several emails to the maintainer of ?xlsx? package but 
unfortunately, he is unresponsive.

Am I allowed to use an alternative package for exporting data only for 
mac users?

Best regards,

Arman

*From: *Arman Shahrisa <mailto:shahrisa.arman at hotmail.com>
*Sent: *Thursday, September 3, 2020 10:59
*To: *Pages, Herve <mailto:hpages at fredhutch.org>; bioc-devel 
<mailto:bioc-devel at r-project.org>
*Subject: *RE: [Bioc-devel] Java version issue on Bioconductor test platform

Hi Herve,

The last response in the previous topic suggested that the maintainer 
has already fixed the problem on GitHub but not CRAN.

https://stat.ethz.ch/pipermail/bioc-devel/2020-May/016791.html 
<https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_pipermail_bioc-2Ddevel_2020-2DMay_016791.html&d=DwMGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=9S9mNopR4XSbGqAMmUModsQcHeIRaBXsJKTU1m2Rf0M&s=d-jhcrcDtaq6GiLWUPPiebqAN_Z2spl69fFwkzz3ERs&e=>

This is from May and the problem still persists. I?ll try contacting the 
maintainer of xlsx.

Best regards,

Arman

*From: *Pages, Herve <mailto:hpages at fredhutch.org>
*Sent: *Thursday, September 3, 2020 01:06
*To: *Arman Shahrisa <mailto:shahrisa.arman at hotmail.com>; bioc-devel 
<mailto:bioc-devel at r-project.org>
*Subject: *Re: [Bioc-devel] Java version issue on Bioconductor test platform

Hi Arman,

You already asked about this in May:
https://stat.ethz.ch/pipermail/bioc-devel/2020-May/016788.html 
<https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_pipermail_bioc-2Ddevel_2020-2DMay_016788.html&d=DwMGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=9S9mNopR4XSbGqAMmUModsQcHeIRaBXsJKTU1m2Rf0M&s=Ojb8pDAdLSGLFTQfhBx0i20SzBueTg8Owpd3LiW5Wts&e=>

Have you followed up with the xlsx maintainers as suggested by Llu?s?

Cheers,
H.

On 8/29/20 11:12, Arman Shahrisa wrote:

 > Hi to all,
 >
 > I?m maintainer of the package ?cbaf?. I have been monitoring reports

for my package for months. I know there were some issues with mac 
server. However, it seems that error shown from mac server regarding my 
package is caused by some incompatible java application installed on 
Bioconductor server. I would be grateful if you would kindly check this 
issue for me.

 >
 > Best wishes,
 > Arman
 >
 >
 >??????? [[alternative HTML version deleted]]
 >
 >
 > _______________________________________________
 > Bioc-devel at r-project.org mailing list
 >

https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=uVvhfQ6BPTCSmaMBY75Fju40h5GVVRhL_eXtphggDFg&s=6pEzMultxNqzC8mdCzk_UKXBj7S18C9lchZUWdKOXlc&e=

-- 
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org
Phone:? (206) 667-5791
Fax:??? (206) 667-1319

Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

Arman Shahrisa

Sat, Sep 12, 2020 2:02 AM #

Dear Herve,

Thank you very much for recommending the openxlsx package. It looks like that
it also supports multiple sheets per file. I?ll try replacing xlsx with openxlsx package
for all platforms.

Best regards,
Arman


From: Pages, Herve<mailto:hpages at fredhutch.org>
Sent: Thursday, September 10, 2020 21:52
To: Arman Shahrisa<mailto:shahrisa.arman at hotmail.com>; bioc-devel<mailto:bioc-devel at r-project.org>
Subject: Re: FW: [Bioc-devel] Java version issue on Bioconductor test platform

Hi Arman,

Sure, if xlsx is broken and won't be fixed, use something else. Maybe
try openxlsx? Similar to xlsx but doesn't require Java:

   https://CRAN.R-project.org/package=openxlsx

But why would you use something else on Mac only? It's easier from a
maintenance point of view if you use the same code on all platforms,
whenever possible.

Best,
H.

On 9/9/20 11:06, Arman Shahrisa wrote:

Hi to all,

I have sent several emails to the maintainer of ?xlsx? package but
unfortunately, he is unresponsive.

Am I allowed to use an alternative package for exporting data only for
mac users?

Best regards,

Arman

*From: *Arman Shahrisa <mailto:shahrisa.arman at hotmail.com>
*Sent: *Thursday, September 3, 2020 10:59
*To: *Pages, Herve <mailto:hpages at fredhutch.org>; bioc-devel
<mailto:bioc-devel at r-project.org>
*Subject: *RE: [Bioc-devel] Java version issue on Bioconductor test platform

Hi Herve,

The last response in the previous topic suggested that the maintainer
has already fixed the problem on GitHub but not CRAN.

https://stat.ethz.ch/pipermail/bioc-devel/2020-May/016791.html
<https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_pipermail_bioc-2Ddevel_2020-2DMay_016791.html&d=DwMGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=9S9mNopR4XSbGqAMmUModsQcHeIRaBXsJKTU1m2Rf0M&s=d-jhcrcDtaq6GiLWUPPiebqAN_Z2spl69fFwkzz3ERs&e=>

This is from May and the problem still persists. I?ll try contacting the
maintainer of xlsx.

Best regards,

Arman

*From: *Pages, Herve <mailto:hpages at fredhutch.org>
*Sent: *Thursday, September 3, 2020 01:06
*To: *Arman Shahrisa <mailto:shahrisa.arman at hotmail.com>; bioc-devel
<mailto:bioc-devel at r-project.org>
*Subject: *Re: [Bioc-devel] Java version issue on Bioconductor test platform

Hi Arman,

You already asked about this in May:
https://stat.ethz.ch/pipermail/bioc-devel/2020-May/016788.html
<https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_pipermail_bioc-2Ddevel_2020-2DMay_016788.html&d=DwMGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=9S9mNopR4XSbGqAMmUModsQcHeIRaBXsJKTU1m2Rf0M&s=Ojb8pDAdLSGLFTQfhBx0i20SzBueTg8Owpd3LiW5Wts&e=>

Have you followed up with the xlsx maintainers as suggested by Llu?s?

Cheers,
H.

On 8/29/20 11:12, Arman Shahrisa wrote:

 > Hi to all,
 >
 > I?m maintainer of the package ?cbaf?. I have been monitoring reports

for my package for months. I know there were some issues with mac
server. However, it seems that error shown from mac server regarding my
package is caused by some incompatible java application installed on
Bioconductor server. I would be grateful if you would kindly check this
issue for me.

 >
 > Best wishes,
 > Arman
 >
 >
 >        [[alternative HTML version deleted]]
 >
 >
 > _______________________________________________
 > Bioc-devel at r-project.org mailing list
 >

https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=uVvhfQ6BPTCSmaMBY75Fju40h5GVVRhL_eXtphggDFg&s=6pEzMultxNqzC8mdCzk_UKXBj7S18C9lchZUWdKOXlc&e=

--
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

--
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319