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seahtrue
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Hi @vcjdeboer
Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.
The DESCRIPTION file for this package is:
Package: seahtrue
Type: Package
Title: Seahtrue revives XF data for structured data analysis
Version: 0.99.0
Authors@R: c(
person("Vincent", "de Boer",
email = "[email protected]",
role = c("cre", "aut"),
comment=c(ORCID="0000-0001-9928-1698")),
person("Gerwin", "Smits", role = c("aut")),
person("Xiang", "Zhang", role = c("aut"))
)
Description:
Seahtrue organizes oxygen consumption and extracellular acidification
analysis data from experiments performed on an XF analyzer
into structured nested tibbles.This allows for detailed processing of
raw data and advanced data visualization and statistics. Seahtrue introduces
an open and reproducible way to analyze these XF experiments.
It uses file paths to .xlsx files. These .xlsx files are supplied by the
userand are generated by the user in the Wave software from Agilent from the
assay result files (.asyr). The .xlsx file contains different sheets of
important data for the experiment;
1. Assay Information - Details about how the experiment was set up.
2. Rate Data - Information about the OCR and ECAR rates.
3. Raw Data - The original raw data collected during the experiment.
4. Calibration Data - Data related to calibrating the instrument.
Seahtrue focuses on getting the specific data needed for analysis.
Once this data is extracted, it is prepared for calculations through
preprocessing. To make sure everything is accurate, both the initial data
and the preprocessed data go through thorough checks.
biocViews: CellBasedAssays, FunctionalPrediction, DataRepresentation,
DataImport, CellBiology, Cheminformatics,
Metabolomics, MicrotitrePlateAssay, Visualization,
QualityControl, BatchEffect, ExperimentalDesign,
Preprocessing, GO
License: Artistic-2.0
Encoding: UTF-8
LazyData: false
Suggests:
rmarkdown,
testthat (>= 3.0.0),
Imports:
dplyr (>= 1.1.2),
readxl (>= 1.4.1),
logger (>= 0.2.2),
tidyxl (>= 1.0.8),
knitr (>= 1.40),
purrr (>= 0.3.5),
tidyr (>= 1.3.0),
lubridate (>= 1.8.0),
stringr (>= 1.4.1),
tibble (>= 3.1.8),
validate (>= 1.1.1),
rlang (>= 1.0.0),
glue (>= 1.6.2),
cli (>= 3.4.1),
janitor (>= 2.2.0),
ggplot2 (>= 3.5.0),
RColorBrewer (>= 1.1.3),
colorspace (>= 2.1.0),
forcats (>= 1.0.0),
ggridges (>= 0.5.6),
readr (>= 2.1.5),
scales (>= 1.3.0),
sessioninfo (>= 1.2.2),
details (>= 0.3.0),
knitr (>= 1.46.0)
RoxygenNote: 7.3.1
Depends:
R (>= 4.2.0)
VignetteBuilder: knitr
StagedInstall: no
URL: https://vcjdeboer.github.io/seahtrue/
BugReports: https://vcjdeboer.github.io/seahtrue/issues
I'm getting the following ERROR when trying to build your package
R CMD build seahtrue
* checking for file 'seahtrue/DESCRIPTION' ... OK
* preparing 'seahtrue':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘inspect.Rmd’ using rmarkdown
Quitting from lines at lines 163-170 [unnamed-chunk-13] (inspect.Rmd)
Error: processing vignette 'inspect.Rmd' failed with diagnostics:
file is not in PNG format
--- failed re-building ‘inspect.Rmd’
--- re-building ‘plot.Rmd’ using rmarkdown
INFO [2024-05-20 09:05:00] Start reviving
INFO [2024-05-20 09:05:10] Finished reviving
Warning in grid.Call.graphics(C_polygon, x$x, x$y, index) :
semi-transparency is not supported on this device: reported only once per page
Warning in grid.Call.graphics(C_polygon, x$x, x$y, index) :
semi-transparency is not supported on this device: reported only once per page
Warning in grid.Call.graphics(C_polygon, x$x, x$y, index) :
semi-transparency is not supported on this device: reported only once per page
INFO [2024-05-20 09:05:12] Start glueing
INFO [2024-05-20 09:05:12] Start reviving
INFO [2024-05-20 09:05:22] Finished reviving
INFO [2024-05-20 09:05:22] Start reviving
INFO [2024-05-20 09:05:31] Finished reviving
INFO [2024-05-20 09:05:31] Start reviving
INFO [2024-05-20 09:05:40] Finished reviving
INFO [2024-05-20 09:05:40] Finished glueing
Warning in grid.Call.graphics(C_polygon, x$x, x$y, index) :
semi-transparency is not supported on this device: reported only once per page
Warning in grid.Call.graphics(C_polygon, x$x, x$y, index) :
semi-transparency is not supported on this device: reported only once per page
Quitting from lines at lines 280-285 [unnamed-chunk-18] (plot.Rmd)
Error: processing vignette 'plot.Rmd' failed with diagnostics:
file is not in PNG format
--- failed re-building ‘plot.Rmd’
--- re-building ‘revive.Rmd’ using rmarkdown
INFO [2024-05-20 09:05:42] Start reviving
INFO [2024-05-20 09:05:51] Finished reviving
Quitting from lines at lines 75-80 [unnamed-chunk-2] (revive.Rmd)
Error: processing vignette 'revive.Rmd' failed with diagnostics:
file is not in PNG format
--- failed re-building ‘revive.Rmd’
--- re-building ‘seahtrue.Rmd’ using rmarkdown
Quitting from lines at lines 48-53 [unnamed-chunk-2] (seahtrue.Rmd)
Error: processing vignette 'seahtrue.Rmd' failed with diagnostics:
file is not in PNG format
--- failed re-building ‘seahtrue.Rmd’
SUMMARY: processing the following files failed:
‘inspect.Rmd’ ‘plot.Rmd’ ‘revive.Rmd’ ‘seahtrue.Rmd’
Error: Vignette re-building failed.
Execution halted
I will also mention, I have a .Rprofile that sets certain settings such as options(useFancyQuotes=FALSE) . It appears that when trying to build your package my settings are being overwritten. Changing user settings is not allowed and should be corrected.
thank you for trying to build the package! I updated the vignettes to use the BiocStyle and removed the vignettes that were initially created for a pkgdown site that was deployed on github. Also, I deleted the .Rprofile file from the package.
I suggest running this in a clean environment as I still cannot build the package locally
R CMD build seahtrue
* checking for file 'seahtrue/DESCRIPTION' ... OK
* preparing 'seahtrue':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘seahtrue.Rmd’ using rmarkdown
INFO [2024-05-28 10:55:52] Start reviving
INFO [2024-05-28 10:56:02] Finished reviving
Quitting from lines 195-200 [unnamed-chunk-12] (seahtrue.Rmd)
Error: processing vignette 'seahtrue.Rmd' failed with diagnostics:
file is not in PNG format
--- failed re-building ‘seahtrue.Rmd’
SUMMARY: processing the following file failed:
‘seahtrue.Rmd’
Error: Vignette re-building failed.
Execution halted
Thanks again for building. I reproduced the error in the vignette building by running in a clean docker/rstudio environment, and found that likely the sessioninfo or details package caused the error. Now I used the default sytemsInfo() from utils instead of these packages. This fix results in a good build of the vignette. I hope that this is now solved.
Your package has been added to git.bioconductor.org to continue the pre-review process. A build report will be posted shortly. Please fix any ERROR and WARNING in the build report before a reviewer is assigned or provide a justification on why you feel the ERROR or WARNING should be granted an exception.
IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. All changes should be pushed to git.bioconductor.org moving forward. It is required to push a version bump to git.bioconductor.org to trigger a new build report.
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Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Single Package Builder.
On one or more platforms, the build results were: "ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details.
The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): seahtrue_0.99.0.tar.gz
Links above active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/seahtrue to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
A reviewer has been assigned to your package for an indepth review. Please respond accordingly to any further comments from the reviewer.
Received a valid push on git.bioconductor.org; starting a build for commit id: 5b70c6c248e2aac701a0c3f0612cc3cca3e94007
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Single Package Builder.
On one or more platforms, the build results were: "WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details.
The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): seahtrue_0.99.1.tar.gz
Links above active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/seahtrue to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Thanks for this submission.
R CMD check
Please do not ignore these 2 R CMD check NOTEs:
* checking R code for possible problems ... NOTE
calc_background: no visible binding for global variable ‘flagged_well’
calc_background: no visible binding for global variable ‘group’
calc_background: no visible binding for global variable ‘well’
calc_background: no visible binding for global variable ‘tick’
calc_background: no visible binding for global variable ‘O2_em_corr’
calc_background: no visible binding for global variable ‘pH_em_corr’
calc_background: no visible binding for global variable ‘O2_mmHg’
calc_background: no visible binding for global variable ‘pH’
calc_background: no visible binding for global variable
‘pH_em_corr_corr’
convert_timestamp: no visible binding for global variable ‘timestamp’
convert_timestamp: no visible binding for global variable ‘times’
convert_timestamp: no visible binding for global variable
‘totalMinutes’
convert_timestamp: no visible binding for global variable ‘minutes’
get_platelayout_data: no visible binding for global variable ‘well’
get_platelayout_data: no visible binding for global variable
‘my_values’
get_timing_info: no visible binding for global variable ‘measurement’
get_timing_info: no visible binding for global variable ‘tick’
get_timing_info: no visible binding for global variable ‘timescale’
get_timing_info: no visible binding for global variable ‘st’
get_timing_info: no visible binding for global variable ‘end’
get_timing_info: no visible binding for global variable ‘lagged’
get_timing_info: no visible binding for global variable
‘number_of_ticks’
get_timing_info: no visible binding for global variable ‘per_meas’
get_timing_info: no visible binding for global variable ‘wait_mix’
get_xf_assayinfo: no visible binding for global variable ‘parameter’
get_xf_assayinfo: no visible binding for global variable ‘value’
get_xf_assayinfo: no visible binding for global variable ‘tick’
get_xf_assayinfo: no visible binding for global variable ‘timestamp’
get_xf_assayinfo: no visible binding for global variable ‘.’
get_xf_flagged: no visible binding for global variable ‘address’
get_xf_inj: no visible binding for global variable ‘command_name’
get_xf_inj: no visible binding for global variable ‘command_index’
get_xf_inj: no visible binding for global variable ‘measurement’
get_xf_inj: no visible binding for global variable ‘instruction_name’
get_xf_raw: no visible binding for global variable ‘.’
get_xf_raw: no visible binding for global variable ‘pH_corrected_em’
get_xf_raw: no visible binding for global variable ‘O2_corrected_em’
glue_xfplates: no visible binding for global variable ‘.’
missing_strings: no visible binding for global variable ‘value’
missing_strings: no visible binding for global variable ‘valid_codes’
plot_line_per_well: no visible binding for global variable ‘param’
plot_line_per_well: no visible binding for global variable
‘measurement’
plot_line_per_well: no visible binding for global variable ‘interval’
plot_line_per_well: no visible binding for global variable ‘time_wave’
plot_line_per_well: no visible global function definition for ‘head’
plot_line_per_well: no visible global function definition for ‘tail’
plot_line_per_well: no visible binding for global variable ‘injection’
plot_line_per_well: no visible binding for global variable ‘well’
plot_line_per_well: no visible binding for global variable ‘group’
plot_ribbon_per_meas_and_group: no visible binding for global variable
‘param’
plot_ribbon_per_meas_and_group: no visible binding for global variable
‘measurement’
plot_ribbon_per_meas_and_group: no visible binding for global variable
‘interval’
plot_ribbon_per_meas_and_group: no visible binding for global variable
‘time_wave’
plot_ribbon_per_meas_and_group: no visible global function definition
for ‘head’
plot_ribbon_per_meas_and_group: no visible global function definition
for ‘tail’
plot_ribbon_per_meas_and_group: no visible binding for global variable
‘injection’
plot_ribbon_per_meas_and_group: no visible global function definition
for ‘quantile’
plot_ribbon_per_meas_and_group: no visible binding for global variable
‘group’
plot_ribbon_per_meas_and_group: no visible binding for global variable
‘X100’
plot_ribbon_per_meas_and_group: no visible binding for global variable
‘X0’
plot_ribbon_per_meas_and_group: no visible binding for global variable
‘X50’
plot_ribbon_per_meas_and_group: no visible binding for global variable
‘X25’
plot_ribbon_per_meas_and_group: no visible binding for global variable
‘X75’
preprocess_xf_raw: no visible binding for global variable ‘well’
preprocess_xf_raw: no visible binding for global variable ‘plate_id’
preprocess_xf_raw: no visible binding for global variable ‘measurement’
preprocess_xf_raw: no visible binding for global variable ‘tick’
preprocess_xf_raw: no visible binding for global variable ‘timescale’
preprocess_xf_raw: no visible binding for global variable ‘minutes’
preprocess_xf_raw: no visible binding for global variable ‘group’
preprocess_xf_raw: no visible binding for global variable ‘interval’
preprocess_xf_raw: no visible binding for global variable ‘injection’
preprocess_xf_raw: no visible binding for global variable ‘O2_em_corr’
preprocess_xf_raw: no visible binding for global variable ‘pH_em_corr’
preprocess_xf_raw: no visible binding for global variable ‘O2_mmHg’
preprocess_xf_raw: no visible binding for global variable ‘pH’
preprocess_xf_raw: no visible binding for global variable
‘pH_em_corr_corr’
preprocess_xf_raw: no visible binding for global variable
‘O2_em_corr_bkg’
preprocess_xf_raw: no visible binding for global variable
‘pH_em_corr_bkg’
preprocess_xf_raw: no visible binding for global variable ‘O2_mmHg_bkg’
preprocess_xf_raw: no visible binding for global variable ‘pH_bkgd’
preprocess_xf_raw: no visible binding for global variable
‘pH_em_corr_corr_bkg’
preprocess_xf_raw: no visible binding for global variable
‘bufferfactor’
preprocess_xf_raw: no visible binding for global variable ‘cell_n’
preprocess_xf_raw: no visible binding for global variable
‘flagged_well’
preprocess_xfplate: no visible binding for global variable ‘plate_id’
preprocess_xfplate: no visible binding for global variable
‘filepath_seahorse’
preprocess_xfplate: no visible binding for global variable ‘date_run’
preprocess_xfplate: no visible binding for global variable
‘date_processed’
preprocess_xfplate: no visible binding for global variable ‘assay_info’
preprocess_xfplate: no visible binding for global variable
‘injection_info’
preprocess_xfplate: no visible binding for global variable ‘data’
preprocess_xfplate: no visible binding for global variable ‘rate_data’
read_xfplate: no visible binding for global variable ‘.’
relevel_group_names: no visible binding for global variable ‘group’
sketch_assimilate_rate: no visible binding for global variable
‘plate_id’
sketch_assimilate_rate: no visible binding for global variable
‘rate_data’
sketch_assimilate_rate: no visible binding for global variable
‘measurement’
sketch_assimilate_rate: no visible binding for global variable
‘injection’
sketch_assimilate_rate: no visible binding for global variable
‘interval’
sketch_assimilate_rate: no visible binding for global variable ‘well’
sketch_assimilate_rate: no visible binding for global variable ‘group’
sketch_assimilate_rate: no visible binding for global variable ‘cell_n’
sketch_assimilate_rate: no visible binding for global variable
‘flagged_well’
sketch_assimilate_rate: no visible binding for global variable ‘rate’
sketch_assimilate_raw: no visible binding for global variable
‘plate_id’
sketch_assimilate_raw: no visible binding for global variable
‘raw_data’
sketch_assimilate_raw: no visible binding for global variable
‘measurement’
sketch_assimilate_raw: no visible binding for global variable ‘well’
sketch_assimilate_raw: no visible binding for global variable ‘group’
sketch_assimilate_raw: no visible binding for global variable
‘emission’
sketch_assimilate_raw: no visible binding for global variable
‘group_id’
sketch_plate: no visible binding for global variable ‘well’
sketch_plate: no visible binding for global variable ‘column’
sketch_plate: no visible binding for global variable ‘group’
sketch_rate: no visible binding for global variable ‘group’
sketch_rate: no visible binding for global variable ‘cell_n’
sketch_rate: no visible binding for global variable ‘well’
sketch_rate: no visible binding for global variable ‘my_param’
sketch_rate: no visible binding for global variable ‘.’
validate_O2_pH_levels : validate_ticks: no visible binding for global
variable ‘data’
validate_O2_pH_levels : validate_ticks: no visible binding for global
variable ‘validate’
validate_O2_pH_levels : validate_ticks: no visible binding for global
variable ‘well’
validate_O2_pH_levels : get_failed_values: no visible binding for
global variable ‘failed’
validate_O2_pH_levels : get_failed_values: no visible binding for
global variable ‘well’
validate_O2_pH_levels : get_failed_values: no visible binding for
global variable ‘values’
validate_O2_pH_levels: no visible binding for global variable ‘well’
validate_O2_pH_levels: no visible binding for global variable
‘measurement’
validate_O2_pH_levels: no visible binding for global variable ‘.’
validate_O2_pH_levels: no visible binding for global variable
‘n_failed’
validate_O2_pH_levels: no visible binding for global variable ‘param’
validate_O2_pH_levels: no visible binding for global variable ‘label’
validate_for_NA: no visible binding for global variable ‘.’
validate_for_NA: no visible binding for global variable ‘well’
validate_for_NA: no visible binding for global variable ‘measurement’
validate_for_NA: no visible binding for global variable ‘tick’
validate_for_NA: no visible binding for global variable ‘group’
validate_preprocessed: no visible global function definition for
‘in_range’
validate_preprocessed: no visible binding for global variable ‘O2_mmHg’
validate_preprocessed: no visible binding for global variable ‘pH’
validate_preprocessed: no visible global function definition for
‘is_complete’
validate_preprocessed: no visible binding for global variable ‘well’
validate_preprocessed: no visible binding for global variable
‘measurement’
validate_preprocessed: no visible binding for global variable ‘tick’
validate_preprocessed: no visible binding for global variable
‘timescale’
validate_preprocessed: no visible binding for global variable ‘minutes’
validate_preprocessed: no visible binding for global variable ‘group’
validate_preprocessed: no visible binding for global variable
‘interval’
validate_preprocessed: no visible binding for global variable
‘injection’
validate_preprocessed: no visible binding for global variable
‘pH_em_corr’
validate_preprocessed: no visible binding for global variable
‘O2_em_corr’
validate_preprocessed: no visible binding for global variable
‘pH_em_corr_corr’
validate_preprocessed: no visible binding for global variable
‘O2_em_corr_bkg’
validate_preprocessed: no visible binding for global variable
‘pH_em_corr_bkg’
validate_preprocessed: no visible binding for global variable
‘O2_mmHg_bkg’
validate_preprocessed: no visible binding for global variable ‘pH_bkgd’
validate_preprocessed: no visible binding for global variable
‘pH_em_corr_corr_bkg’
validate_preprocessed: no visible binding for global variable
‘bufferfactor’
validate_preprocessed: no visible binding for global variable ‘cell_n’
validate_preprocessed: no visible binding for global variable
‘flagged_well’
validate_well_number: no visible binding for global variable ‘well’
validatie_tick_is_linear: no visible binding for global variable
‘measurement’
validatie_tick_is_linear: no visible binding for global variable ‘tick’
validatie_tick_is_linear: no visible binding for global variable ‘well’
validatie_tick_is_linear: no visible binding for global variable
‘group’
verify_xf_rate: no visible binding for global variable ‘well’
verify_xf_rate: no visible binding for global variable ‘group’
verify_xf_rate: no visible binding for global variable ‘ocr’
verify_xf_rate: no visible binding for global variable ‘measurement’
verify_xf_rate: no visible binding for global variable ‘time_wave’
verify_xf_rate: no visible binding for global variable ‘OCR_wave’
verify_xf_rate: no visible binding for global variable ‘OCR_wave_bc’
verify_xf_rate: no visible binding for global variable ‘ECAR_wave’
verify_xf_rate: no visible binding for global variable ‘ECAR_wave_bc’
Undefined global functions or variables:
. ECAR_wave ECAR_wave_bc O2_corrected_em O2_em_corr O2_em_corr_bkg
O2_mmHg O2_mmHg_bkg OCR_wave OCR_wave_bc X0 X100 X25 X50 X75 address
assay_info bufferfactor cell_n column command_index command_name data
date_processed date_run emission end failed filepath_seahorse
flagged_well group group_id head in_range injection injection_info
instruction_name interval is_complete label lagged measurement
minutes my_param my_values n_failed number_of_ticks ocr pH pH_bkgd
pH_corrected_em pH_em_corr pH_em_corr_bkg pH_em_corr_corr
pH_em_corr_corr_bkg param parameter per_meas plate_id quantile rate
rate_data raw_data st tail tick time_wave times timescale timestamp
totalMinutes valid_codes validate value values wait_mix well
Consider adding
importFrom("stats", "end", "quantile")
importFrom("utils", "data", "head", "tail", "timestamp")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) glue_xfplates.Rd:37: Lost braces; missing escapes or markup?
37 | Other {read functions}:
| ^
checkRd: (-1) revive_xfplate.Rd:38: Lost braces; missing escapes or markup?
38 | Other {read functions}:
| ^
Vignette
Right now the output of sessionInfo() is part of the 4.1.4 section:
It should be in its own final section instead.
Also why use echo=FALSE here?
```{r echo=FALSE}
sessionInfo()
```
Wouldn't it make more sense to let the user know what command was used to produce this output?
Thanks, H.
Received a valid push on git.bioconductor.org; starting a build for commit id: cd579289b7440a616ad79ab451589586e0a22e12
Hi @hpages
Thanks for the comments! I corrected the two notes from R CMD check. I used the .data$ approach for most, since this was also in other recently accepted packages (eg tidytof). If not possible, I changed tidy coding to base R coding.
Furthermore, I corrected the layout and echo=false mistakes in the vignette.
Vincent
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Single Package Builder.
On one or more platforms, the build results were: "WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details.
The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): seahtrue_0.99.2.tar.gz
Links above active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/seahtrue to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Hi @vcjdeboer,
Thanks for addressing the 2 R CMD check NOTEs.
There's also this R CMD check NOTE:
* checking whether package ‘seahtrue’ can be installed ... NOTE
Found the following notes/warnings:
Non-staged installation was used
See ‘/home/hpages/pkgreviews/seahtrue.review/seahtrue.Rcheck/00install.out’ for details.
The reason you get this note is because you have StagedInstall: no in your DESCRIPTION file. Any reason the package needs to use non-staged installation? If not, then please remove the StagedInstall: no line.
Also please note that the output of sessionInfo() is still part of the 4.1 subsection of the vignette, which is a non-conventional place to put it:
As mentioned previously, it should be in its own final section instead (i.e. section 5 in this case).
Another peculiarity of the vignette layout is that 4.1 is the only subsection of section 4. The layout will be clearer/simpler if you remove the unnecessary level of nesting. Concretely this means moving sub-subsections 4.1.1 to 4.1.5 one level up so they become subsections 4.1 to 4.5. Hope this makes sense.
Best, H.
Dear @hpages, thanks for the response. I have changed the section titles and deleted the stagedInstall:no line. I also pushed these commits to the bioconductor. Many thanks, Vincent
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