[Bioc-devel] EXTERNAL: ERROR: Avoid references to external hosting platforms
Marcel Ramos
m@rce|@r@mo@perez @end|ng |rom ro@we||p@rk@org
Mon Oct 18 02:26:26 CEST 2021
Hi Marta,
I don't see the error when running `BiocCheck::BiocCheck()` on my end
(InterCellar version 1.1.0).
I am using Bioc devel 3.14 and R 4.1.1.
For now, you can safely ignore those false positives and open an issue on
https://github.com/Bioconductor/BiocCheck/issues if you are still
getting an error.
If interested, please see the BiocCheck output below.
Best regards,
Marcel
---
> Rdev -e "BiocCheck::BiocCheck()"
R version 4.1.1 Patched (2021-09-30 r81006) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocCheck::BiocCheck()
This is BiocCheck version 1.29.16. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
* Checking if other packages can import this one...
* ERROR: Packages providing 1 object(s) used in this package should
be imported in the NAMESPACE file, otherwise packages importing
this package may fail.
package::object in function()
stats::complete.cases in read.cellchat()
* Checking to see if we understand object initialization...
* NOTE: Consider clarifying how 89 object(s) are initialized. Maybe
they are part of a data set loaded with data(), or perhaps part
of an object referenced in with() or within().
function (object)
annotateGO (go_linkage_type)
annotateGO (domain)
annotateGO (int_pair)
annotateGO (geneA)
annotateGO (geneB)
annotateGO (gene_symbol)
annotateGO (go_id)
annotateGO (geneA.1)
annotateGO (geneB.4)
annotatePathways (int_pair)
annotatePathways (geneA)
annotatePathways (geneB)
combineAnnotations (int_pair)
combineAnnotations (functional_term)
createBarPlot1_ggplot (clusters)
createBarPlot1_ggplot (n_int)
createBarPlot1_ggplot (type)
createBarPlot2_ggplot (Clusters)
createBarPlot2_ggplot (Num_int)
getBack2BackBarplot (condition)
getBack2BackBarplot (n_int)
getBack2BackBarplot (clusters)
getBack2BackBarplot (type)
getBack2BackBarplot (diff_c1_c2)
getBarplotDF (clustA)
getBarplotDF (clustB)
getBarplotDF (int.type)
getBarplotDF2 (clustA)
getBarplotDF2 (clustB)
getClusterNetwork (clustA)
getClusterNetwork (clustB)
getClusterNetwork (score)
getClusterSize (clustA)
getClusterSize (clustB)
getDotPlot_selInt (clustA)
getDotPlot_selInt (clustB)
getDotPlot_selInt (int_pair)
getDotPlot_selInt (cluster_pair)
getDotPlot_selInt (score)
getGeneTable (int_pair)
getGeneTable (geneA)
getGeneTable (geneB)
getGeneTable (typeA)
getGeneTable (typeB)
getGeneTable (annotation_strategy)
getGeneTable (pathway_cellchat)
getGeneTable (annotation_cellchat)
getGeneTable (evidence_cellchat)
getGeneTable (uniprotswissprot)
getGeneTable (ensembl_gene_id)
getGeneTable (hgnc_symbol)
getIntFlow (typeA)
getIntFlow (typeB)
getIntFlow (clustA)
getIntFlow (clustB)
getRadarPlot (legend)
getRankedTerms (functional_term)
getRankedTerms (uniq_score)
getRankedTerms (int_pair)
getRankedTerms (avg_uniqueness)
getSunburst (clustA)
getSunburst (int_pair)
getSunburst (clustB)
getUniqueDotplot (int_pair)
getUniqueDotplot (cluster_pair)
getUniqueDotplot (condition)
mod_cluster_verse_server (clustA)
mod_cluster_verse_server (clustB)
mod_cluster_verse_server (score)
mod_cluster_verse_server (int.type)
mod_function_verse_server (GO_id)
mod_function_verse_server (int_pair)
mod_gene_verse_server (scSignalR_specific)
mod_gene_verse_server (annotation_cellchat)
mod_gene_verse_server (pathway_cellchat)
mod_gene_verse_server (int_pair)
mod_gene_verse_server (clustA)
mod_gene_verse_server (clustB)
mod_gene_verse_server (int.type)
mod_int_pair_modules_server (int_pair)
mod_int_pair_modules_server (int_pairModule)
mod_int_pair_modules_server (p_value)
read.CPDBv2 (cluster_pair)
read.CPDBv2 (mean_value)
read.CPDBv2 (interacting_pair)
read.CPDBv2 (p_value)
updateInputLR (typeA)
updateInputLR (typeB)
updateInputLR (int_pair)
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking version number validity...
* Checking R Version dependency...
* Checking package size...
Skipped... only checked on source tarball
* Checking individual file sizes...
* WARNING: The following files are over 5MB in size:
'.git/objects/pack/pack-a1161a04bfe06bb12a006c137aadfb94cb26e254.pack'
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
* NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
vignettes/user_guide.Rmd
* Checking package installation calls in R code...
* Checking for library/require of InterCellar...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
Found in files:
R/fct_function_verse.R (line 346, column 26)
R/fct_int_pair_modules.R (line 227, column 24)
R/fct_int_pair_modules.R (line 228, column 24)
R/fct_upload_custom.R (line 15, column 29)
R/fct_upload_custom.R (line 17, column 29)
R/fct_upload.R (line 91, column 48)
R/fct_upload.R (line 94, column 48)
R/fct_upload.R (line 160, column 48)
R/fct_upload.R (line 163, column 48)
R/fct_upload.R (line 191, column 27)
R/fct_upload.R (line 202, column 27)
R/fct_upload.R (line 379, column 32)
R/fct_upload.R (line 383, column 32)
R/golem_utils_server.R (line 21, column 6)
R/utils_upload.R (line 38, column 35)
R/utils_upload.R (line 40, column 35)
* NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
R/mod_upload_custom.R (line 157, column 34)
R/mod_upload_custom.R (line 166, column 32)
R/mod_upload_custom.R (line 174, column 32)
R/mod_upload.R (line 179, column 32)
R/mod_upload.R (line 188, column 32)
R/mod_upload.R (line 196, column 32)
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2
times)
suppressWarnings() in R/mod_function_verse.R (line 164, column
26)
suppressWarnings() in R/mod_upload.R (line 213, column 22)
* Checking function lengths.............................
* NOTE: Recommended function length <= 50 lines.
There are 29 functions > 50 lines.
The longest 5 functions are:
mod_gene_verse_server() (R/mod_gene_verse.R, line 152): 551
lines
_anonymous_.153() (R/mod_gene_verse.R, line 153): 549 lines
mod_int_pair_modules_server() (R/mod_int_pair_modules.R, line
157): 512 lines
_anonymous_.164() (R/mod_int_pair_modules.R, line 164): 504
lines
mod_cluster_verse_server() (R/mod_cluster_verse.R, line 250):
460 lines
* Checking man page documentation...
* NOTE: Consider adding runnable examples to the following man
pages which document exported objects:
run_app.Rd
* NOTE: Usage of dontrun{} / donttest{} found in man page examples.
2% of man pages use one of these cases.
Found in the following files:
run_app.Rd
* NOTE: Use donttest{} instead of dontrun{}.
Found in the following files:
run_app.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 326 lines (4%) are > 80 characters
long.
First 6 lines:
R/app_server.R:21 rv <- reactiveValues(input.data = NULL,
filt.data =...
R/app_server.R:39 clust.data <-
mod_cluster_verse_server("cluster_v...
R/app_server.R:45 gene.data <-
mod_gene_verse_server("gene_verse_ui...
R/app_server.R:51 func.data <-
mod_function_verse_server("function_...
R/app_ui.R:16 dashboardHeader(title =
span(img(src = ...
R/app_ui.R:25 href="ht...
* NOTE: Consider multiples of 4 spaces for line indents, 2531
lines(34%) are not.
First 6 lines:
R/app_config.R:8 system.file(..., package = "InterCellar")
R/app_config.R:22 value,
R/app_config.R:23 config = Sys.getenv("R_CONFIG_ACTIVE",
"default"),
R/app_config.R:24 use_parent = TRUE
R/app_config.R:26 config::get(
R/app_config.R:32 )
See http://bioconductor.org/developers/how-to/coding-style/
See styler package: https://cran.r-project.org/package=styler as
described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking for bioc-devel mailing list subscription...
* NOTE: Cannot determine whether maintainer is subscribed to the
bioc-devel mailing list (requires admin credentials). Subscribe
here: https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
Summary:
ERROR count: 1
WARNING count: 1
NOTE count: 12
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.14/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheck FAILED.
$error
[1] "Packages providing 1 object(s) used in this package should be
imported in the NAMESPACE file, otherwise packages importing this
package may fail."
$warning
[1] "The following files are over 5MB in size:
'.git/objects/pack/pack-a1161a04bfe06bb12a006c137aadfb94cb26e254.pack'"
$note
[1] "Consider clarifying how 89 object(s) are initialized. Maybe they
are part of a data set loaded with data(), or perhaps part of an object
referenced in with() or within()."
[2] " 'sessionInfo' not found in vignette(s)"
[3] " Avoid sapply(); use vapply()"
[4] " Avoid redundant 'stop' and 'warn*' in signal conditions"
[5] "Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)"
[6] "Recommended function length <= 50 lines."
[7] "Consider adding runnable examples to the following man pages
which document exported objects:"
[8] "Usage of dontrun{} / donttest{} found in man page examples."
[9] "Use donttest{} instead of dontrun{}."
[10] "Consider shorter lines; 326 lines (4%) are > 80 characters long."
[11] "Consider multiples of 4 spaces for line indents, 2531 lines(34%)
are not."
[12] "Cannot determine whether maintainer is subscribed to the
bioc-devel\nmailing list (requires admin credentials). Subscribe
here:\nhttps://stat.ethz.ch/mailman/listinfo/bioc-devel"
----
On 10/16/21 6:20 AM, Marta Interlandi wrote:
> Dear Marcel,
>
> I have updated BiocCheck to version 1.29.16, but the error persists.
> Here my lines of code that are causing this issue, in red the lines
> indicated by BiocCheck:
>
> dropdownMenu(type="tasks",
> icon=icon("info"),
> badgeStatus=NULL,
> headerText="Check out",
> notificationItem(
> text="InterCellar",
> icon=icon("github"),
> status="primary",
> href="https://github.com/martaint/InterCellar
> <https://secure-web.cisco.com/13EM8WN4sg9TPE_mRHA3XhLcgRiPAZnSaYXuDyd31DF6tVXGznKttF7a_TQ3qkTNDJ1T9BieebuO1PDE5h5-5FbJxFVciVVsQCQ4ZzkB1ID2tRchkUtbT1Eexi3Ymdx_oP7ofK0EgxUjBUtgJo0eVH9WUm9uRkzCKwO00XrlNXUsPvWvD5CB6gX_LJ6-Bp_YXArfptCPQXpazPSCdE6THzFhVDUFbT1eXXIXzxwF5QAUfrVTWhwgLnBAHqZl7J_QP2LTOwRN3dv2d7wJAa1Rn_TThrvGlPh58M3wcildjKgipasszzBq58sDYT-aGkLiP/https%3A%2F%2Fgithub.com%2Fmartaint%2FInterCellar>"
> ),
> notificationItem(
> text="InterCellar-reproducibility",
> icon=icon("github"),
> status="primary",
> href="https://github.com/martaint/InterCellar-reproducibility
> <https://secure-web.cisco.com/1V9uFOQ1rnml0F7UCooserQqX2TGusszy2SHG9RpCd-iWF_S7IdltUepuqw8a8zlnxJZ7d1oQRAdjAzMisLM3y392gW-Fvhmv3_njfTB6cjrfeX38csHrTAKwwurEo15wRDhq_rOrwp33T8CokQiEgjwzIn3UJ9cucpAVJihGYoA421tb1gd0dzqTnh8xDoFEsfdm__83oKghIe5TH3Wb1EqBAzuf3eSdTcBgK6bl0bR9lGQGLfQzzGfxpN8FWGLFcrqhL6VV_fHwQpfRZ267LbpkMTJ0BNTwHkI00LJmMuq-7m2YvCs1NyxzR8ls2M5q/https%3A%2F%2Fgithub.com%2Fmartaint%2FInterCellar-reproducibility>"
> ),
> notificationItem(
> text="Bioconductor package",
> icon=icon("cube"),
> status="primary",
>
> href="https://bioconductor.org/packages/InterCellar/"
> )
> These are part of the app UI.
>
> Thank you very much for taking a look at this!
>
> Best regards,
>
> Marta
>
> On Fri, 15 Oct 2021 at 00:47, Marcel Ramos <MA40231 using roswellpark.org>
> wrote:
>
> Hi Marta,
>
> Thank you for bringing this to our attention.
> We've made an update to BiocCheck to minimize these false positives.
> Please use BiocCheck version >= 1.29.16 which should propagate in a
> day or so.
>
> Best regards,
>
> Marcel
>
> On 10/14/21 10:39 AM, Marta Interlandi wrote:
> > Hi everybody,
> >
> > My package *InterCellar *is currently getting the error "Avoid
> references
> > to external hosting platforms" when running BiocCheck.
> > The error is caused by href items pointing towards the github
> repos of the
> > package itself, in the form of clickable links (the package is a
> Shiny app).
> > These 3 links however are not used to get any data, but are
> simply nice
> > features for the shiny app users.
> >
> > Do you have any suggestions on how I could still include these links
> > without getting an error?
> >
> > Thank you so much for your help!!
> >
> > Best regards,
> >
> > Marta
> >
> > [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioc-devel using r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> <https://secure-web.cisco.com/1fmi1F_2Mk1VRYN_IIN8S6STa2vjXoaLoqmbIahvfFvUxl3CE_B9mMuhGiqFu5MEPla4HPVYsn6cka2yc_muZLW6N_M6unW6m4TTVXuV2afNCHFkyr7OuGvWaSyYXg-PVJqry2DzsaioqlZldgEG-Et1MbZAK4toNd-F1oWSqtsn1CwrEVEZantTY30RRtohNJp76pJTuZLxFPH9Vk1mOHI20lBr6RgtX0NGZinm5WTt2y3kGhdCPBo9zsL4oa1aOfqVSgUU-jTsDkn-qQDWW3HO81hX2sqmUy6QXdIUAfkE-Vg8ODMrpMGiBhNcQoU68/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel>
>
> Marcel Ramos
> Bioconductor Core Team
> Roswell Park Comprehensive Cancer Care
> Dept. of Biostatistics & Bioinformatics
> Elm & Carlton Streets
> Buffalo, New York 14263
>
>
>
> This email message may contain legally privileged
> and/or...{{dropped:2}}
>
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> <https://secure-web.cisco.com/1fmi1F_2Mk1VRYN_IIN8S6STa2vjXoaLoqmbIahvfFvUxl3CE_B9mMuhGiqFu5MEPla4HPVYsn6cka2yc_muZLW6N_M6unW6m4TTVXuV2afNCHFkyr7OuGvWaSyYXg-PVJqry2DzsaioqlZldgEG-Et1MbZAK4toNd-F1oWSqtsn1CwrEVEZantTY30RRtohNJp76pJTuZLxFPH9Vk1mOHI20lBr6RgtX0NGZinm5WTt2y3kGhdCPBo9zsL4oa1aOfqVSgUU-jTsDkn-qQDWW3HO81hX2sqmUy6QXdIUAfkE-Vg8ODMrpMGiBhNcQoU68/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel>
>
---
Marcel Ramos
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Dept. of Biostatistics & Bioinformatics
Elm St. & Carlton St.
Buffalo, New York 14263
This email message may contain legally privileged and/or...{{dropped:4}}
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