[R-pkg-devel] Checksums changed on CRAN without any visible modifications to files.

2018-06-13 Thread Joris Meys 
Dear all,

I have another report of checksums for CRAN packages that changed without
any visible change to the package itself.

https://github.com/easybuilders/easybuild-easyconfigs/pull/6446

At the time of the release of R3.5, pkgmaker was at version 0.22. A bit
after the release, this version was archived and replaced by the new one
(0.27). Somewhere in that process the checksum for the tarball of version
0.22 changed.

The only explanation I can come up with, is that either because of the
release of R3.5 or because of the archiving the tarball was recreated and
has a different timestamp. That's the only way I know a MD5 checksum of a
tarball can change without any change to the files in there.

Anyone knows what is going on here, and how this can be circumvented at the
client side?

Cheers
Joris


-- 
Joris Meys
Statistical consultant

Department of Data Analysis and Mathematical Modelling
Ghent University
Coupure Links 653, B-9000 Gent (Belgium)


tel: +32 (0)9 264 61 79
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Re: [R-pkg-devel] Checksums changed on CRAN without any visible modifications to files.

2018-06-13 Thread Uwe Ligges 




On 13.06.2018 12:45, Joris Meys wrote:

Dear all,

I have another report of checksums for CRAN packages that changed without
any visible change to the package itself.

https://github.com/easybuilders/easybuild-easyconfigs/pull/6446

At the time of the release of R3.5, pkgmaker was at version 0.22. A bit
after the release, this version was archived and replaced by the new one
(0.27). Somewhere in that process the checksum for the tarball of version
0.22 changed.

The only explanation I can come up with, is that either because of the
release of R3.5 or because of the archiving the tarball was recreated and
has a different timestamp. That's the only way I know a MD5 checksum of a
tarball can change without any change to the files in there.

Anyone knows what is going on here, and how this can be circumvented at the
client side?


When CRAN repacks and changes the DESCRIPTION file, the checksums 
change, of course.


Best,
Uwe Ligges








Cheers
Joris




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Re: [R-pkg-devel] Checksums changed on CRAN without any visible modifications to files.

2018-06-13 Thread Joris Meys 
On Wed, Jun 13, 2018 at 3:16 PM, Uwe Ligges  wrote:

>
> When CRAN repacks and changes the DESCRIPTION file, the checksums change,
> of course.
>
> Best,
> Uwe Ligges
>
>
Dear Uwe,

I understood that from the previous issue. In this case however, none of
the files -including the DESCRIPTION file- were changed. Am I right in
suspecting that a package is repacked when moved to the archive? I suspect
that the tool used to repack the package is using gzip, and it is possible
to repack without adding a timestamp as explained here :

https://serverfault.com/questions/110208/different-md5sums-for-same-tar-contents

I can explain the different checksums when some things are changed to our
HPC sysadmins, but they have -understandibly- difficulties with checksums
changing for released source tarballs. Is it possible to adapt the
archiving so that at least for identical tarballs the md5 sums remain the
same? Or if you have other suggestions to deal with this without having to
change hardcoded checksums in the easybuild repos, that would be very
welcome too.

Cheers
Joris

-- 
Joris Meys
Statistical consultant

Department of Data Analysis and Mathematical Modelling
Ghent University
Coupure Links 653, B-9000 Gent (Belgium)


tel: +32 (0)9 264 61 79
---
Biowiskundedagen 2017-2018
http://www.biowiskundedagen.ugent.be/

---
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Re: [R-pkg-devel] R Markdown and tables in Word

2018-06-13 Thread Jason Serviss 
Hi Shakell,

You have sent your enquiry to the R package development mailing list. You will 
most likely get more help and relevant answers if you send to the R-help 
mailing list since here we are mostly (totally) focused on package development.

You can find the mailing lists and their descriptions here: 
https://www.r-project.org/mail.html

Regards,
Jason


On 13 Jun 2018, at 16:31, Shakeel Suleman 
mailto:shakeel.sule...@phe.gov.uk>> wrote:

I am relatively new to R and was wondering if someone could advise me on 
presenting tables in R Markdown for Word. I would like to present a simple 
table of counts, with column 1 representing name of an organisation (and last 
row called "All organisations") and another four columns representing the most 
recent four week period (e.g. week 21, 22, 23, 24) and a final total column, as 
illustrated below. The actual data is just counts (e.g. 4, 5, 8, widgets 
produced, number of people off sick etc).

My question is: can this be done to a publication quality standard. I have 
tried Pander, but that adds "Sum" instead of All Organisations and 4 Week Total 
and doesn't look particularly good.



Week



20

21

22

23

4 week total

Organisation

6

6

1

1

14

ABC

2

4

1

5

12

DCE

0

5

1

5

11

EFG

3

6

3

5

17

HIJ

1

8

3

2

14

All Organizations

12

29

9

18

68




Kind regards,

Shakeel


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[R-pkg-devel] R Markdown and tables in Word

2018-06-13 Thread Shakeel Suleman 
I am relatively new to R and was wondering if someone could advise me on 
presenting tables in R Markdown for Word. I would like to present a simple 
table of counts, with column 1 representing name of an organisation (and last 
row called "All organisations") and another four columns representing the most 
recent four week period (e.g. week 21, 22, 23, 24) and a final total column, as 
illustrated below. The actual data is just counts (e.g. 4, 5, 8, widgets 
produced, number of people off sick etc).

My question is: can this be done to a publication quality standard. I have 
tried Pander, but that adds "Sum" instead of All Organisations and 4 Week Total 
and doesn't look particularly good.



Week



20

21

22

23

4 week total

Organisation

6

6

1

1

14

ABC

2

4

1

5

12

DCE

0

5

1

5

11

EFG

3

6

3

5

17

HIJ

1

8

3

2

14

All Organizations

12

29

9

18

68




Kind regards,

Shakeel


**
The information contained in the EMail and any attachments is confidential and 
intended solely and for the attention and use of the named addressee(s). It may 
not be disclosed to any other person without the express authority of Public 
Health England, or the intended recipient, or both. If you are not the intended 
recipient, you must not disclose, copy, distribute or retain this message or 
any part of it. This footnote also confirms that this EMail has been swept for 
computer viruses by Symantec.Cloud, but please re-sweep any attachments before 
opening or saving. http://www.gov.uk/PHE
**
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Re: [R-pkg-devel] R Markdown and tables in Word

2018-06-13 Thread Duncan Murdoch 

On 13/06/2018 10:52 AM, Jason Serviss wrote:

Hi Shakell,

You have sent your enquiry to the R package development mailing list. You will 
most likely get more help and relevant answers if you send to the R-help 
mailing list since here we are mostly (totally) focused on package development.

You can find the mailing lists and their descriptions here: 
https://www.r-project.org/mail.html


Shakeel was (incorrectly) sent here from there.  Since then other advice 
has appeared:  probably an RStudio forum or Stack Overflow is his best bet.


Duncan Murdoch



Regards,
Jason


On 13 Jun 2018, at 16:31, Shakeel Suleman 
mailto:shakeel.sule...@phe.gov.uk>> wrote:

I am relatively new to R and was wondering if someone could advise me on presenting 
tables in R Markdown for Word. I would like to present a simple table of counts, with 
column 1 representing name of an organisation (and last row called "All 
organisations") and another four columns representing the most recent four week 
period (e.g. week 21, 22, 23, 24) and a final total column, as illustrated below. The 
actual data is just counts (e.g. 4, 5, 8, widgets produced, number of people off sick 
etc).

My question is: can this be done to a publication quality standard. I have tried Pander, 
but that adds "Sum" instead of All Organisations and 4 Week Total and doesn't 
look particularly good.



Week



20

21

22

23

4 week total

Organisation

6

6

1

1

14

ABC

2

4

1

5

12

DCE

0

5

1

5

11

EFG

3

6

3

5

17

HIJ

1

8

3

2

14

All Organizations

12

29

9

18

68




Kind regards,

Shakeel


**
The information contained in the EMail and any attachments is confidential and 
intended solely and for the attention and use of the named addressee(s). It may 
not be disclosed to any other person without the express authority of Public 
Health England, or the intended recipient, or both. If you are not the intended 
recipient, you must not disclose, copy, distribute or retain this message or 
any part of it. This footnote also confirms that this EMail has been swept for 
computer viruses by Symantec.Cloud, but please re-sweep any attachments before 
opening or saving. http://www.gov.uk/PHE
**
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