bug#39885: Bioconductor tarballs are not archived

[Timothy Sample]

Hi Simon,

Simon Tournier  writes:

> Just to be sure: we are speaking about Bioconductor only, right?

I took “this report” to be the PoG report not the bug report.  My
mistake!  Sorry for the confusion.


-- Tim

bug#39885: Bioconductor tarballs are not archived

[Simon Tournier]

Hi,

On ven., 16 févr. 2024 at 10:14, Timothy Sample  wrote:

>> Can we consider that this report is now done?  Because:
>>
>> 1. SWH supports ExtID and nar hash lookup.
>>
>> 2. Missing origins are currently ingested by SWH.
>>(via specific sources.json)
>
> I think that would be jumping the gun a little bit.
>
> In some sense, the report is only *done* when “stored” hits 100% (or
> close to it, with the remainder being stuff we are pretty sure no longer
> exists).  This won’t happen just because of your second point there.

Just to be sure: we are speaking about Bioconductor only, right?


> When the historical “sources.json” is loaded, things will be much, much,
> better, sure.  Sources will still be missing, though.

Yeah, sources will still be missing but I expect that Bioconductor will
be not.  The only issue is about “annotation” and maybe “experiment”.
However, here we are hitting the boundary between code and data:
annotation and experiment might be very large and potentially skipped by
SWH and they contain few if no code but plain data.

We can still discuss what to do here; in this already long thread. :-)
Or we can open another thread for this specific case about Bioconductor
annotation and experiment.

>   To me, this is an
> invitation to more subtle analysis, like weighing sources by their
> “importance” in the package graph.  Then there’s still shortcomings with
> Disarchive that have to be resolved (which is work best guided by
> numbers in the report).

Yeah.  But that seems a large scope than Bioconductor case, no?


> Also, it will always be a good idea to verify that things are working.
> Ideally this could be simpler (leveraging ExtID lookup) and continuous.

Indeed, checking that all Bioconductor sources can be extracted from
SWH+Disarchive seems the path forward closing this report. :-)

Cheers,
simon

bug#39885: Bioconductor tarballs are not archived

[Timothy Sample]

Simon Tournier  writes:

> Cool!
>
> Can we consider that this report is now done?  Because:
>
> 1. SWH supports ExtID and nar hash lookup.
>
> 2. Missing origins are currently ingested by SWH.
>(via specific sources.json)

I think that would be jumping the gun a little bit.

In some sense, the report is only *done* when “stored” hits 100% (or
close to it, with the remainder being stuff we are pretty sure no longer
exists).  This won’t happen just because of your second point there.
When the historical “sources.json” is loaded, things will be much, much,
better, sure.  Sources will still be missing, though.  To me, this is an
invitation to more subtle analysis, like weighing sources by their
“importance” in the package graph.  Then there’s still shortcomings with
Disarchive that have to be resolved (which is work best guided by
numbers in the report).

Also, it will always be a good idea to verify that things are working.
Ideally this could be simpler (leveraging ExtID lookup) and continuous.


-- Tim

bug#39885: Bioconductor tarballs are not archived

[Simon Tournier]

Hi,

On ven., 19 janv. 2024 at 09:46, Timothy Sample  wrote:

>   $ git clone https://git.ngyro.com/preservation-of-guix
>   $ cd preservation-of-guix
>   $ wget https://ngyro.com/pog-reports/latest/pog.db
>
>   [Wait a long time because my server is slw.]
>
>   $ guile -L . etc/sources.scm pog.db > missing-sources.json

Cool!

Can we consider that this report is now done?  Because:

1. SWH supports ExtID and nar hash lookup.

2. Missing origins are currently ingested by SWH.
   (via specific sources.json)


Cheers,
simon

bug#39885: Bioconductor tarballs are not archived

[Ludovic Courtès]

Hi Timothy,

Timothy Sample  skribis:

> Hello,
>
> Ludovic Courtès  writes:
>
>> As for past tarballs, #swh-devel comrades say we could send them a list
>> of URLs and they’d create “Save Code Now” requests on our behalf (we
>> cannot do it ourselves since the site doesn’t accept plain tarballs.)
>>
>> Any volunteer to write a script that’d generate a list of Bioconductor
>> content-addressed URLs (the bordeaux.guix.gnu.org/file ones) for say the
>> past couple of years?
>
> Sorry I’m a little late to this party, but I wrote a similar script a
> while ago.  It creates a “sources.json” file of all the sources that the
> PoG database analyzed and found missing in SWH.  It only covers what PoG
> monitors (which is *almost* everything, but not quite).

Excellent!

> With some modifications, I used it to generate the attached list of
> Bioconductor sources (based off of recent, unpublished PoG data).  I’ve
> also attached the modifications in case anyone is curious or wants to
> make a similar list.  I will publish the PoG database soon (today?), so
> maybe wait for that before generating any lists.

After discussing it on #swh-devel, I filed this issue:

  https://gitlab.softwareheritage.org/swh/infra/sysadm-environment/-/issues/5222

Tim, you were planning to offer a larger list of missing sources
extracted from the PoG database, right?

Thank you!

Ludo’.

bug#39885: Bioconductor tarballs are not archived

[Timothy Sample]

Hello,

Ludovic Courtès  writes:

> As for past tarballs, #swh-devel comrades say we could send them a list
> of URLs and they’d create “Save Code Now” requests on our behalf (we
> cannot do it ourselves since the site doesn’t accept plain tarballs.)
>
> Any volunteer to write a script that’d generate a list of Bioconductor
> content-addressed URLs (the bordeaux.guix.gnu.org/file ones) for say the
> past couple of years?

Sorry I’m a little late to this party, but I wrote a similar script a
while ago.  It creates a “sources.json” file of all the sources that the
PoG database analyzed and found missing in SWH.  It only covers what PoG
monitors (which is *almost* everything, but not quite).

  $ git clone https://git.ngyro.com/preservation-of-guix
  $ cd preservation-of-guix
  $ wget https://ngyro.com/pog-reports/latest/pog.db

  [Wait a long time because my server is slw.]

  $ guile -L . etc/sources.scm pog.db > missing-sources.json

With some modifications, I used it to generate the attached list of
Bioconductor sources (based off of recent, unpublished PoG data).  I’ve
also attached the modifications in case anyone is curious or wants to
make a similar list.  I will publish the PoG database soon (today?), so
maybe wait for that before generating any lists.


-- Tim



bioconductor-sources.json.gz
Description: Binary data
diff --git a/etc/sources.scm b/etc/sources.scm
index 71d157d..515cf00 100644
--- a/etc/sources.scm
+++ b/etc/sources.scm
@@ -1,5 +1,5 @@
 ;;; Preservation of Guix
-;;; Copyright © 2022 Timothy Sample 
+;;; Copyright © 2022, 2024 Timothy Sample 
 ;;;
 ;;; This file is part of Preservation of Guix.
 ;;;
@@ -61,6 +61,7 @@ FROM fods f
 WHERE f.algorithm = 'sha256'
 AND (fr.reference LIKE '\"%'
 OR fr.reference LIKE '(\"%')
+AND fr.reference LIKE '%bioconductor.org%'
 AND NOT fr.is_error
 AND f.is_in_swh IS NOT NULL
 AND NOT f.is_in_swh")
@@ -85,22 +86,25 @@ Subresource Integrity metadata value."
   (define b64 (base64-encode bv))
   (string-append "sha256-" b64))
 
-(define (web-reference-urls reference)
+(define (web-reference-filename reference)
   (define uris
 (match (call-with-input-string reference read)
   ((urls ...) (map string->uri urls))
   (url (list (string->uri url)
-  (append-map (lambda (uri)
-(map uri->string
- (maybe-expand-mirrors uri %mirrors)))
-  uris))
+  (or (any (lambda (uri)
+ (and (string-suffix? "bioconductor.org" (uri-host uri))
+  (basename (uri-path uri
+   uris)
+  (error "Not a 'bioconductor.org' refernce" reference)))
 
 (define (record->url-source rec)
   (match-let ((#(digest reference) rec))
-(let ((urls (web-reference-urls reference))
-  (integrity (nix-base32-sha256->subresource-integrity digest)))
+(let* ((filename (web-reference-filename reference))
+   (url (string-append "https://bordeaux.guix.gnu.org/file/;
+   filename "/sha256/" digest))
+   (integrity (nix-base32-sha256->subresource-integrity digest)))
   `(("type" . "url")
-("urls" . ,(list->vector urls))
+("urls" . ,(vector url))
 ("integrity" . ,integrity)
 
 (define (lookup-missing-sources db)

bug#39885: Bioconductor tarballs are not archived

[Simon Tournier]

Hi,

On Wed, 10 Jan 2024 at 13:42, Ricardo Wurmus  wrote:

> Do we have a list of desired tarballs?

I made one. :-)  I will share the manifest once a bit more polish. ;-)

Roughly, until 3.11 -- for earlier, I am still fighting with
time-machine -- and only the versions right before a Bioconductor
upgrade (and sadly not the version after such upgrade that, for many
have disappeared from Bioconductor).  If you have them, cool!  Well,
for now, I am speaking about all the Bioconductor packages except
annotations for these Guix revisions:

--8<---cut here---start->8---
git log --format="%P %s" --after=2019-04-30 \
| grep -i -E 'bioconductor' | grep -i -E '(update|upgrade)' \
| cut -f1 -d' ' \
| head -8
--8<---cut here---end--->8---

And for instance, I have this kind of sources.json.

--8<---cut here---start->8---
{
  "sources": [
{
  "type": "url",
  "urls": [

"https://bordeaux.guix.gnu.org/file/progeny_1.22.0.tar.gz/sha256/047x6by3xa15gvi3kny5pkqxaq8d2kzcfi55ic5j7a351715l6l7;,

"https://ci.guix.gnu.org/file/progeny_1.22.0.tar.gz/sha256/047x6by3xa15gvi3kny5pkqxaq8d2kzcfi55ic5j7a351715l6l7;,

"https://bioconductor.org/packages/3.17/bioc/src/contrib/progeny_1.22.0.tar.gz;,

"https://tarballs.nixos.org/sha256/047x6by3xa15gvi3kny5pkqxaq8d2kzcfi55ic5j7a351715l6l7;
  ],
  "integrity": "sha256-hxpawgllqCMLi6VEx/4UDWHV8bzF2znifiWoPvwy/RA=",
  "outputHashAlgo": "sha256",
  "outputHashMode": "flat"
},
{
  "type": "url",
  "urls": [

"https://bordeaux.guix.gnu.org/file/AWFisher_1.14.0.tar.gz/sha256/1c6rr1z1rhvn8w1kb3nnjlfacfr22vwm1rsa1xqm2hmghs01bq4x;,

"https://ci.guix.gnu.org/file/AWFisher_1.14.0.tar.gz/sha256/1c6rr1z1rhvn8w1kb3nnjlfacfr22vwm1rsa1xqm2hmghs01bq4x;,

"https://bioconductor.org/packages/3.17/bioc/src/contrib/AWFisher_1.14.0.tar.gz;,

"https://tarballs.nixos.org/sha256/1c6rr1z1rhvn8w1kb3nnjlfacfr22vwm1rsa1xqm2hmghs01bq4x;
  ],
  "integrity": "sha256-neAVgIavQlFxD0rnUPkWIjumHJXWjjUDR3bDHH7I2bA=",
  "outputHashAlgo": "sha256",
  "outputHashMode": "flat"
},
--8<---cut here---end--->8---

Where the URL for ci.guix is incorrect, I guess.

Cheers,
simon

bug#39885: Bioconductor tarballs are not archived

[Ricardo Wurmus]

Ludovic Courtès  writes:

> I my previous message, I wrote:
>
>> As for past tarballs, #swh-devel comrades say we could send them a list
>> of URLs and they’d create “Save Code Now” requests on our behalf (we
>> cannot do it ourselves since the site doesn’t accept plain tarballs.)
>
> Were you able to retrieve some of these?  What are the chances of
> success?

Do we have a list of desired tarballs?  I still have an archived
/gnu/store from before we moved the shared cluster installation at the
MDC to different storage.  It might contain old tarballs that we no
longer have elsewhere.

-- 
Ricardo

bug#39885: Bioconductor tarballs are not archived

[Ludovic Courtès]

Hi!

Simon Tournier  skribis:

>> I was wondering whether we’re now doing better for Bioconductor
>> tarballs.  The answer, based on small sample, seems to be “not quite”:

[...]

> but, now the past reads,
>
> $ for url in 
> https://bioconductor.org/packages/release/bioc/src/contrib/BiocNeighbors_1.20.0.tar.gz
>  \
>  
> https://bioconductor.org/packages/3.18/bioc/src/contrib/BiocNeighbors_1.20.0.tar.gz
>  ;  \
>   do guix download $url ;done

Thanks for investigating & explaining!

I my previous message, I wrote:

> As for past tarballs, #swh-devel comrades say we could send them a list
> of URLs and they’d create “Save Code Now” requests on our behalf (we
> cannot do it ourselves since the site doesn’t accept plain tarballs.)

Were you able to retrieve some of these?  What are the chances of
success?

> Hence the discussion we had: switch from url-fetch to git-fetch.
> However, after some investigations, it does not seem straightforward:
> The main issue being the almost automatic current updater.  See for
> details [2].

[...]

> https://issues.guix.gnu.org/msgid/878rnwuemq@elephly.net

Indeed, thanks for the link.  I agree that long-term moving to
‘git-fetch’ sounds preferable, but there are quite a few obstacles to
overcome.

Ludo’.

bug#39885: Bioconductor tarballs are not archived

[Simon Tournier]

Hi,

On Fri, 22 Dec 2023 at 14:40, Ludovic Courtès  wrote:

>> guix build: error: build of 
>> `/gnu/store/q9ggmh5a9bzmnr49p10x1w9sv6pzjarv-BiocNeighbors_1.4.1.tar.gz.drv' 
>> failed

First thing first, please note that we are speaking about tag 1.4.1 and
not 1.20.0.  And this 1.4.1 is gone from “our” infra since… ?? That’s
one of the things I do not like with Guix: I never know what to expect
from the infra.  Anyway, I have my list of TODOs for improving the
annoyances (I and maybe others have :-)); stay tuned. ;-)

Considering the state of “our” infra and how Bioconductor manages the
tarballs, many tarballs are lost forever, sadly.  Although the content
is still around, I guess.


> I was wondering whether we’re now doing better for Bioconductor
> tarballs.  The answer, based on small sample, seems to be “not quite”:

Thanks for diving into this.


>  has entries like:
>
> --8<---cut here---start->8---
> {
>   "type": "url",
>   "urls": [
> 
> "https://bioconductor.org/packages/release/bioc/src/contrib/BiocNeighbors_1.20.0.tar.gz;,
> 
> "https://bioconductor.org/packages/3.18/bioc/src/contrib/BiocNeighbors_1.20.0.tar.gz;,
> 
> "https://bordeaux.guix.gnu.org/file/BiocNeighbors_1.20.0.tar.gz/sha256/0a5wg099fgwjbzd6r3mr4l02rcmjqlkdcz1w97qzwx1mir41fmas;,
> 
> "https://ci.guix.gnu.org/file/BiocNeighbors_1.20.0.tar.gz/sha256/0a5wg099fgwjbzd6r3mr4l02rcmjqlkdcz1w97qzwx1mir41fmas;,
> 
> "https://tarballs.nixos.org/sha256/0a5wg099fgwjbzd6r3mr4l02rcmjqlkdcz1w97qzwx1mir41fmas;
>   ],
>   "integrity": "sha256-WlUXSI41dP7xSTx81ibFsrIsACW5jmzaX5I/lxJ4vCg=",
>   "outputHashAlgo": "sha256",
>   "outputHashMode": "flat"
> },
> --8<---cut here---end--->8---

Please note that Bioconductor 3.18 released BiocNeighbors v1.20.0 but
then updated to v1.20.1 still under Bioconductor 3.18 and Ricardo did
this update with 5673484cbc2ed74c61ae81d623646fa7829fbc32.  On a side
note, between the Bioconductor update and the update on our side, there
is a mismatch where the source of r-biocneighbors is unreachable.

Other said, post-update on our side,

--8<---cut here---start->8---
$ zcat sources.json | jq | grep BiocNeighbors | grep bioconductor | sed 
's/"//g' | sed 's/,//g'

https://bioconductor.org/packages/release/bioc/src/contrib/BiocNeighbors_1.20.1.tar.gz

https://bioconductor.org/packages/3.18/bioc/src/contrib/BiocNeighbors_1.20.1.tar.gz

$ for url in $(zcat sources.json | jq | grep BiocNeighbors | grep bioconductor 
| sed 's/"//g' | sed 's/,//g'); \
 do guix download $url ;done

Starting download of /tmp/guix-file.STc9fQ
>From 
>https://bioconductor.org/packages/release/bioc/src/contrib/BiocNeighbors_1.20.1.tar.gz...
 …_1.20.1.tar.gz  1015KiB   
  60.3MiB/s 00:00 ▕██▏ 100.0%
/gnu/store/nxab1pskh9zcjspczph6jcs5fk79pb7k-BiocNeighbors_1.20.1.tar.gz
0w7hd6w0lmj1jaaq9zd5gwnnpkzcr0byqm5q584wjg4xgvsb981j

Starting download of /tmp/guix-file.aZFRLv
>From 
>https://bioconductor.org/packages/3.18/bioc/src/contrib/BiocNeighbors_1.20.1.tar.gz...
 …_1.20.1.tar.gz  1015KiB   
  63.5MiB/s 00:00 ▕██▏ 100.0%
/gnu/store/nxab1pskh9zcjspczph6jcs5fk79pb7k-BiocNeighbors_1.20.1.tar.gz
0w7hd6w0lmj1jaaq9zd5gwnnpkzcr0byqm5q584wjg4xgvsb981j
--8<---cut here---end--->8---

but, now the past reads,

--8<---cut here---start->8---
$ for url in 
https://bioconductor.org/packages/release/bioc/src/contrib/BiocNeighbors_1.20.0.tar.gz
 \
 
https://bioconductor.org/packages/3.18/bioc/src/contrib/BiocNeighbors_1.20.0.tar.gz
 ;  \
  do guix download $url ;done

> > 
Starting download of /tmp/guix-file.MUB3ow
>From 
>https://bioconductor.org/packages/release/bioc/src/contrib/BiocNeighbors_1.20.0.tar.gz...
download failed 
"https://bioconductor.org/packages/release/bioc/src/contrib/BiocNeighbors_1.20.0.tar.gz;
 404 "Not Found"

Starting download of /tmp/guix-file.MUB3ow
>From 
>https://web.archive.org/web/20240102105016/https://bioconductor.org/packages/release/bioc/src/contrib/BiocNeighbors_1.20.0.tar.gz...
download failed 
"https://web.archive.org/web/20240102105016/https://bioconductor.org/packages/release/bioc/src/contrib/BiocNeighbors_1.20.0.tar.gz;
 404 "NOT FOUND"
Trying to use Disarchive to assemble /tmp/guix-file.MUB3ow...
could not find its Disarchive specification
failed to download "/tmp/guix-file.MUB3ow" from 
"https://bioconductor.org/packages/release/bioc/src/contrib/BiocNeighbors_1.20.0.tar.gz;
guix download: error: 
https://bioconductor.org/packages/release/bioc/src/contrib/BiocNeighbors_1.20.0.tar.gz:
 download failed

Starting download 

bug#39885: Bioconductor tarballs are not archived

[Ludovic Courtès]

Hello!

zimoun  skribis:

> Since 2020, I provided several examples of breakage with bug#39885 [1].
> Here another one:
>
> $ guix time-machine --commit=77e2de365497bf4c8b81cbd78624f78293490485 \
>-- build r-biocneighbors -S

[...]

> Starting download of 
> /gnu/store/zgf7x09kgiqbvj0dmhplxi1xzpljxd7k-BiocNeighbors_1.4.1.tar.gz
>>From 
>>https://web.archive.org/web/20220718175152/https://bioconductor.org/packages/release/bioc/src/contrib/BiocNeighbors_1.4.1.tar.gz...
> download failed 
> "https://web.archive.org/web/20220718175152/https://bioconductor.org/packages/release/bioc/src/contrib/BiocNeighbors_1.4.1.tar.gz;
>  404 "NOT FOUND"
> Trying to use Disarchive to assemble 
> /gnu/store/zgf7x09kgiqbvj0dmhplxi1xzpljxd7k-BiocNeighbors_1.4.1.tar.gz...
> could not find its Disarchive specification
> failed to download 
> "/gnu/store/zgf7x09kgiqbvj0dmhplxi1xzpljxd7k-BiocNeighbors_1.4.1.tar.gz" from 
> ("https://bioconductor.org/packages/release/bioc/src/contrib/BiocNeighbors_1.4.1.tar.gz;
>  
> "https://bioconductor.org/packages/3.10/bioc/src/contrib/Archive/BiocNeighbors_1.4.1.tar.gz;)
> builder for 
> `/gnu/store/q9ggmh5a9bzmnr49p10x1w9sv6pzjarv-BiocNeighbors_1.4.1.tar.gz.drv' 
> failed to produce output path 
> `/gnu/store/zgf7x09kgiqbvj0dmhplxi1xzpljxd7k-BiocNeighbors_1.4.1.tar.gz'
> build of 
> /gnu/store/q9ggmh5a9bzmnr49p10x1w9sv6pzjarv-BiocNeighbors_1.4.1.tar.gz.drv 
> failed
> View build log at 
> '/var/log/guix/drvs/q9/ggmh5a9bzmnr49p10x1w9sv6pzjarv-BiocNeighbors_1.4.1.tar.gz.drv.gz'.
> guix build: error: build of 
> `/gnu/store/q9ggmh5a9bzmnr49p10x1w9sv6pzjarv-BiocNeighbors_1.4.1.tar.gz.drv' 
> failed
>
> Well, several comments:
>
>  1. Berlin or Bordeaux do not have it as substitutes,
>  2. Diasarchive does not have it,
>  3. Many others neither.

I was wondering whether we’re now doing better for Bioconductor
tarballs.  The answer, based on small sample, seems to be “not quite”:

--8<---cut here---start->8---
$ guix lint -c archival $(guix package -A ^r-bioc | cut -f1)
gnu/packages/bioconductor.scm:19708:12: r-biocbaseutils@1.4.0: Disarchive entry 
refers to non-existent SWH directory '726af85395d163b5a21e52e4df1bf18aa0072f6b'
gnu/packages/bioconductor.scm:19752:12: r-bioccheck@1.38.0: Disarchive entry 
refers to non-existent SWH directory '12cfedcbc27005a3fb7e01c5c4b727e0116f596f'
gnu/packages/bioconductor.scm:16892:5: r-biocfilecache@2.10.1: Disarchive entry 
refers to non-existent SWH directory '6a2d6d909a7cedd56e96f5a98770dee8d220'
gnu/packages/bioconductor.scm:4540:12: r-biocgenerics@0.48.1: Disarchive entry 
refers to non-existent SWH directory '6f19ea14f46dbc75909b77bc08e9023daae6fb9e'
gnu/packages/bioconductor.scm:19785:5: r-biocgraph@1.64.0: Disarchive entry 
refers to non-existent SWH directory '977ff052b4e6c948af7af0fc14ae61f71427cb1a'
gnu/packages/bioconductor.scm:21524:6: r-biocio@1.12.0: Disarchive entry refers 
to non-existent SWH directory '29d8fef9a5b386384f20513c612f1e34f6118532'
gnu/packages/bioconductor.scm:13090:5: r-biocneighbors@1.20.0: Disarchive entry 
refers to non-existent SWH directory '6d3728b2dee78cceecdeba0318f3e57b6013d96f'
gnu/packages/bioconductor.scm:19957:5: r-bioconcotk@1.22.0: Disarchive entry 
refers to non-existent SWH directory '251081d4bc3f061ef8e16338eb042ad4c71ed02d'
gnu/packages/bioconductor.scm:20003:5: r-biocor@1.26.0: Disarchive entry refers 
to non-existent SWH directory '0cc9d3dcde06fb353cdd77f3b538845d16a77720'
gnu/packages/bioconductor.scm:6613:12: r-biocparallel@1.36.0: Disarchive entry 
refers to non-existent SWH directory '41e09414898f61655bcc99fdd44d69b0531c0b2d'
gnu/packages/bioconductor.scm:20030:5: r-biocpkgtools@1.20.0: Disarchive entry 
refers to non-existent SWH directory '55de8618648ed16797a8effd5b508c652a5d7cbe'
gnu/packages/bioconductor.scm:20144:5: r-biocset@1.16.0: Disarchive entry 
refers to non-existent SWH directory '1cfa6cac0cb453f2882a35c8f5ae6ddfa713ad2d'
gnu/packages/bioconductor.scm:13276:5: r-biocsingular@1.18.0: Disarchive entry 
refers to non-existent SWH directory '992d3f9d48633fa5d46b9a7640a825054e9538aa'
gnu/packages/bioconductor.scm:19806:12: r-biocstyle@2.30.0: Disarchive entry 
refers to non-existent SWH directory 'bb17c3bd9ac7c373b24782fcfecdde5fa2f0a965'
gnu/packages/bioconductor.scm:22965:5: r-biocthis@1.12.0: Disarchive entry 
refers to non-existent SWH directory '3d08f77aae1e81ce9ca9bb9ae2adf4d4c7421d11'
gnu/packages/bioconductor.scm:4521:5: r-biocversion@3.18.1: source not archived 
on Software Heritage and missing from the Disarchive database
gnu/packages/bioconductor.scm:19830:12: r-biocviews@1.70.0: Disarchive entry 
refers to non-existent SWH directory '47e0877ab988469fc09a37505dd769f9626cac2e'
gnu/packages/bioconductor.scm:20182:5: r-biocworkflowtools@1.28.0: Disarchive 
entry refers to non-existent SWH directory 
'393f3472cc27f632caea3488aef93a7675b403ef'
$ guix describe
Generation 285  Dec 17 2023 23:31:56(current)
  guix 6ab2426
repository URL: