Packages intermittent failtures

Introduction

This report checks if the status of packages on CRAN are due to intermittent failures.

Failures defined as warnings, notes or errors without change on:

• R version used (if not stable the same svn snapshot)

• The package version (Note that CRAN might modify a package without changing the version)

• Their dependencies

Reasons of these failures might be because the packages depend on:

• Random generation numbers

• Flacky external resources

• Other ?

Why is this important?

Because package maintainers of dependencies of that package, R core and CRAN team need to check if the failures are false positives.

This report started because it was suggested as something that the R-repositories working group could help the CRAN team.

Retrieve data

It makes use of tools::CRAN_check_results to retrieve the data.

library("dplyr")
library("tools", include.only = c("package_dependencies", "CRAN_check_results"))
library("flextable", include.only = c("flextable", "autofit"))
# Use a LOCAL environment to check if files can be overwritten on my computer
local_build <- as.logical(Sys.getenv("LOCAL", "FALSE"))
yc <- readRDS("today.RDS")
tc <- CRAN_check_results()
# Added 2023/03/09: sometimes some flavors are reported without status: Omit those
tc <- tc[!is.na(tc$Status),]
if (!interactive() && !local_build) {
  message("Saving today's file.")
  saveRDS(tc, file = "today.RDS")
} 

The checks are from multiple flavors release, devel, old release and patched on multiple machines and configurations.

old_flavors <- readRDS("flavors.RDS")
flavors <- unique(tc$Flavor)
# One flavor now present in all is the r-devel-windows-x86_64: skip
flavors <- setdiff(flavors, "r-devel-windows-x86_64")
proto <- data.frame(r_version = character(),
                    os = character(),
                    architecture = character(),
                    other = character())
flavors_df <- strcapture(
  pattern = "r-([[:alnum:]]+)-([[:alnum:]]+)-([[:alnum:]_\\+]+)-?(.*)", 
  x = flavors,
  proto = proto)

# Extract R version used and svn id
h <- "https://www.r-project.org/nosvn/R.check/%s/ggplot2-00check.html"
links <- sprintf(h, flavors)
extract_revision <- function(x) {
  r <- readLines(x, 12)[12]
  version <- strcapture(pattern = "([[:digit:]]\\.[[:digit:]]\\.[[:digit:]])",  
                        x = r, proto = data.frame(version = character()))
  revision <- strcapture(pattern = "(r[[:digit:]]+)",  x = r,
                         proto = data.frame(revision = character()))
  cbind(version, revision)
}
revision <- data.frame(version = character(),
                       revision = character())
for (i in links) {
  revision <- rbind(revision, extract_revision(i))
}

flavors_df <- cbind(flavors = flavors, flavors_df, revision)
if (!interactive() && !local_build) {
  saveRDS(flavors_df, "flavors.RDS")
}

m <- match(tc$Flavor, flavors_df$flavors)
tc_flavors <- cbind(tc, flavors_df[m, ])
flextable(flavors_df) |> 
  autofit()

flavors	r_version	os	architecture	other	version	revision
r-devel-linux-x86_64-debian-clang	devel	linux	x86_64	debian-clang		r89950
r-devel-linux-x86_64-debian-gcc	devel	linux	x86_64	debian-gcc		r89963
r-devel-linux-x86_64-fedora-clang	devel	linux	x86_64	fedora-clang		r89960
r-devel-linux-x86_64-fedora-gcc	devel	linux	x86_64	fedora-gcc		r89943
r-patched-linux-x86_64	patched	linux	x86_64		4.6.0	r89932
r-release-linux-x86_64	release	linux	x86_64		4.6.0
r-release-macos-arm64	release	macos	arm64		4.6.0
r-release-macos-x86_64	release	macos	x86_64		4.6.0	r89743
r-release-windows-x86_64	release	windows	x86_64		4.6.0
r-oldrel-macos-arm64	oldrel	macos	arm64		4.5.2	r89382
r-oldrel-macos-x86_64	oldrel	macos	x86_64		4.5.2	r89382
r-oldrel-windows-x86_64	oldrel	windows	x86_64		4.5.3

It assumes that the same configuration in one package is used for all. Or in other words that the reports of the configuration (svn revision and version) for the A3 package is the same as for all the other packages.

Warning: This assumption is not always true, but this would require to check each log file on each flavor to verify the R and svn id of each package (which could take too much time and resources).

Overview

Briefly an introduction of how much effort goes into checking

library("ggplot2")
theme_set(theme_minimal())
tc |> 
  filter(!is.na(T_install)) |> 
  ggplot() +
  geom_violin(aes(T_install, Flavor)) +
  scale_x_log10() +
  labs(x = "seconds", title = "Time to install", y = element_blank())

Distribution of install time on each machine.

This means that just to install all the packages on the multiple flavors with a single CPU would take 70 days.

tc |> 
  filter(!is.na(T_check)) |> 
  ggplot() +
  geom_violin(aes(T_check, Flavor), trim = FALSE) +
  scale_x_log10() +
  labs(x = "seconds", title = "Time to check", y = element_blank())

Distribution of checking time on each machine.

This means that to check all the packages on the multiple flavors with a single CPU would take 344 days.

tc |> 
  filter(!is.na(T_total)) |> 
  ggplot() +
  geom_violin(aes(T_total, Flavor)) +
  scale_x_log10() +
  labs(x = "seconds", title = "Time to check and install", y = element_blank())

Distribution of total time on each machine.

This means that to install and check all the packages with a single CPU would take 429 days.

I don’t know the computational cost of 266 days of CPU (every day), but a rough calculation of 2.5 cents per hour means 257.3 dollars daily dedicated to this.

tc |> 
  group_by(Package) |> 
  summarize(Versions = n_distinct(Version)) |> 
  ungroup() |> 
  count(Versions, name = "Packages", sort = TRUE) |> 
  flextable() |> 
  autofit()

Versions	Packages
1	23,400
2	328
3	2

This was surprising, but sometimes checks have multiple versions. Probably when a new version is added and the system don’t catch it for a certain machine.

tc |> 
  group_by(Package) |> 
  summarize(Flavors = n_distinct(Flavor)) |> 
  ungroup() |> 
  count(Flavors, name = "Packages", sort = TRUE) |> 
  flextable() |> 
  autofit()

Flavors	Packages
13	23,472
12	162
11	37
10	31
3	16
8	5
9	5
4	2

Similarly, often packages are only tested on few configurations.

Combining both we can have packages with few configurations that have multiple versions being tested.

tc |> 
  group_by(Package) |> 
  summarize(Versions = as.character(n_distinct(Version)),
            Flavors = n_distinct(Flavor)) |> 
  ungroup() |> 
  count(Flavors, Versions, name = "Packages") |> 
  ggplot() +
  geom_tile(aes(Flavors, Versions, fill = log10(Packages))) +
  scale_x_continuous(expand = expansion())

Most packages are just tested one version.

But focusing on those that have just one version of the package being tested, most of the machines have packages either OK or with some notes.

man_colors <- c("OK" = "green", "NOTE" = "darkgreen", 
                "WARNING" = "yellow", "ERROR" = "red", "FAILURE" = "black")
tc |> 
  group_by(Package) |> 
  filter(n_distinct(Version) == 1) |> 
  ungroup() |> 
  group_by(Flavor) |> 
  count(Status, name = "packages") |> 
  mutate(perc = packages/sum(packages),
         Status = forcats::fct_relevel(Status, names(man_colors))) |> 
  ggplot() + 
  geom_col(aes(perc, Flavor, fill = Status)) +
  scale_x_continuous(expand = expansion(), labels = scales::percent_format()) +
  scale_fill_manual(values = man_colors) +
  labs(title = "Packages check status", x = element_blank())

Most frequent status is OK or NOTE on all machines.

If we look at the most frequent status report for packages we can see this table:

ts <- tc |> 
  group_by(Package) |> 
  filter(n_distinct(Version) == 1) |> 
  count(Status, name = "flavors") |> 
  ungroup() |> 
  tidyr::pivot_wider(values_from = flavors, names_from = Status, 
                     values_fill = 0) |> 
  count(OK, NOTE, WARNING, ERROR, FAILURE, name = "packages", sort = TRUE)
download.file("https://cran.r-project.org/web/packages/packages.rds", 
              destfile = "packages.RDS") # From the help page
ap <- readRDS("packages.RDS") |> 
  as.data.frame() |> 
  distinct(Package, .keep_all = TRUE)
ap_bioc <- available.packages(repos = BiocManager::repositories()[1:5])
ap_bioc <- cbind(ap_bioc, Additional_repositories = NA)
ap_colm <- intersect(colnames(ap), colnames(ap_bioc))
ap <- rbind(ap[, ap_colm], ap_bioc[, ap_colm])
head(ts) |> 
  flextable() |> 
  autofit()

OK	NOTE	WARNING	ERROR	FAILURE	packages
13	0	0	0	0	15,812
11	2	0	0	0	4,316
0	13	0	0	0	1,151
12	0	0	1	0	721
12	1	0	0	0	292
9	4	0	0	0	281

We can see that the most common occurrences are some sort of OK and notes on checks. We can also check the official results on CRAN.

We can see that 2.62%, 1.06%, 0.41%, 0.17%, 0.01% of packages pass all checks without notes.

Now let’s see which of the notes or failures are due to intermittent issues.

Compare

First we need to make sure that we compare the right configurations. They must be the same machine, the same R version and the same svn revision between yesterday and today.

# Compare the previous flavor with today's
m_flavor <- which(flavors_df$flavors %in% old_flavors$flavors)
m_version <- which(flavors_df$version %in% old_flavors$version)
m_revision <- which(flavors_df$revision %in% old_flavors$revision)
tm <- table(c(m_flavor, m_version, m_revision))
compare <- flavors_df$flavors[tm == 3] # Only missing the packages version

All changes

Next, compare the status of the packages if the version of the package is the same.

# Find package on the flavors to compare that haven't changed versions
library("dplyr")
tcc <- filter(tc, Flavor %in% compare) |> 
  select(Flavor, Package, Version, Status) |> 
  arrange(Flavor, Package)
ycc <- filter(yc, Flavor %in% compare) |> 
  select(Flavor, Package, Version, Status) |> 
  arrange(Flavor, Package)

all_checks <- merge(tcc, ycc, by = c("Flavor", "Package"), 
                    suffixes = c(".t", ".y"), all = TRUE) 

possible_packages <- all_checks |> 
  filter(Version.t == Version.y & # Same version
           Status.t != Status.y & # Different status
           !is.na(Status.y) & # No new version or removed package
           !is.na(Status.t)) |> 
  rename(Today = Status.t, Yesterday = Status.y)
possible_packages |> 
  select(Package, Flavor, Today, Yesterday, -Version.t, -Version.y) |> 
  arrange(Package, Flavor) |> 
  flextable() |> 
  autofit()

Package	Flavor	Today	Yesterday
AER	r-oldrel-windows-x86_64	OK	NOTE
CAESAR.Suite	r-oldrel-windows-x86_64	ERROR	OK
CAESAR.Suite	r-release-windows-x86_64	ERROR	OK
CAST	r-release-windows-x86_64	OK	ERROR
CCAMLRGIS	r-release-windows-x86_64	OK	ERROR
CRTspat	r-release-windows-x86_64	OK	ERROR
DIscBIO	r-release-windows-x86_64	OK	ERROR
FracFixR	r-oldrel-windows-x86_64	FAILURE	OK
KOFM	r-oldrel-windows-x86_64	ERROR	OK
MexicoDataAPI	r-release-windows-x86_64	OK	ERROR
MigConnectivity	r-oldrel-windows-x86_64	ERROR	OK
OdysseusCharacterizationModule	r-oldrel-windows-x86_64	OK	ERROR
OpenRange	r-release-windows-x86_64	ERROR	NOTE
ProFAST	r-oldrel-windows-x86_64	ERROR	OK
ProFAST	r-release-windows-x86_64	ERROR	OK
RCPA	r-release-windows-x86_64	OK	ERROR
RTD	r-oldrel-windows-x86_64	ERROR	OK
RcensusPkg	r-release-windows-x86_64	ERROR	OK
Rdpack	r-oldrel-windows-x86_64	OK	NOTE
S7	r-oldrel-windows-x86_64	OK	ERROR
SDPDmod	r-oldrel-windows-x86_64	ERROR	OK
SiMRiv	r-release-windows-x86_64	OK	ERROR
SpaTopic	r-oldrel-windows-x86_64	ERROR	OK
SubtypeDrug	r-oldrel-windows-x86_64	OK	ERROR
SuperLearner	r-release-windows-x86_64	FAILURE	OK
TreeDist	r-oldrel-windows-x86_64	ERROR	OK
TreeDist	r-release-windows-x86_64	ERROR	OK
TriMatch	r-oldrel-windows-x86_64	ERROR	OK
TriMatch	r-release-windows-x86_64	ERROR	OK
TrialSimulator	r-oldrel-windows-x86_64	ERROR	OK
TurtleGraphics	r-release-windows-x86_64	OK	ERROR
amapro	r-release-windows-x86_64	OK	ERROR
aquacultuR	r-release-windows-x86_64	OK	ERROR
arcgisgeocode	r-release-windows-x86_64	OK	ERROR
arcpbf	r-release-macos-arm64	NOTE	OK
autograph	r-oldrel-windows-x86_64	OK	ERROR
awdb	r-release-macos-arm64	NOTE	OK
bapred	r-oldrel-windows-x86_64	ERROR	OK
basksim	r-release-macos-arm64	ERROR	OK
biomod2	r-release-macos-arm64	OK	ERROR
bootPLS	r-release-windows-x86_64	OK	ERROR
boxcoxmix	r-devel-linux-x86_64-fedora-gcc	ERROR	OK
causalBatch	r-oldrel-windows-x86_64	ERROR	OK
centerline	r-release-windows-x86_64	ERROR	OK
chopin	r-oldrel-windows-x86_64	OK	ERROR
circhelp	r-release-macos-arm64	OK	NOTE
classInt	r-release-macos-arm64	OK	ERROR
coFAST	r-oldrel-windows-x86_64	ERROR	OK
coFAST	r-release-windows-x86_64	ERROR	OK
colleyRstats	r-oldrel-windows-x86_64	ERROR	OK
commonmark	r-release-macos-arm64	ERROR	OK
curl	r-release-macos-arm64	ERROR	OK
data.table	r-release-macos-arm64	ERROR	NOTE
dataquieR	r-release-windows-x86_64	OK	ERROR
delimtools	r-oldrel-windows-x86_64	NOTE	OK
dispersionIndicators	r-release-macos-arm64	OK	ERROR
divvy	r-release-windows-x86_64	OK	ERROR
doolkit	r-release-macos-arm64	NOTE	ERROR
dplyr	r-oldrel-windows-x86_64	ERROR	NOTE
ecb	r-release-macos-arm64	OK	ERROR
ediblecity	r-release-windows-x86_64	ERROR	OK
eks	r-release-windows-x86_64	ERROR	OK
eudata	r-oldrel-windows-x86_64	ERROR	OK
eudata	r-release-macos-arm64	ERROR	OK
eudata	r-release-windows-x86_64	ERROR	OK
exactRankTests	r-release-macos-arm64	NOTE	OK
ezplot	r-release-macos-arm64	ERROR	OK
f1pits	r-release-windows-x86_64	ERROR	OK
fcl	r-release-macos-arm64	NOTE	OK
finna	r-release-macos-arm64	ERROR	OK
fioRa	r-release-windows-x86_64	OK	ERROR
forrest	r-release-macos-arm64	OK	NOTE
fozziejoin	r-release-macos-arm64	NOTE	OK
fresh	r-release-macos-arm64	OK	ERROR
getRad	r-release-macos-arm64	ERROR	OK
ggautomap	r-oldrel-windows-x86_64	OK	ERROR
ggdibbler	r-oldrel-windows-x86_64	WARNING	OK
ggdibbler	r-release-macos-arm64	WARNING	OK
ggmapcn	r-oldrel-windows-x86_64	ERROR	OK
ggridges	r-release-macos-arm64	ERROR	OK
ggseg3d	r-oldrel-windows-x86_64	OK	ERROR
git2rdata	r-oldrel-windows-x86_64	ERROR	OK
gitGPT	r-release-macos-arm64	NOTE	OK
golem	r-release-macos-arm64	OK	ERROR
gridExtra	r-release-macos-arm64	ERROR	OK
heck	r-release-macos-arm64	NOTE	OK
hockeystick	r-oldrel-windows-x86_64	OK	ERROR
hyd1d	r-release-macos-arm64	OK	ERROR
icosa	r-release-windows-x86_64	ERROR	OK
jewel	r-release-macos-arm64	ERROR	OK
jlview	r-release-windows-x86_64	ERROR	OK
jrSiCKLSNMF	r-release-windows-x86_64	WARNING	OK
lacrmr	r-release-macos-arm64	OK	ERROR
lang	r-release-macos-arm64	OK	ERROR
lares	r-oldrel-windows-x86_64	OK	ERROR
lifecycle	r-release-macos-arm64	ERROR	OK
llmjson	r-release-macos-arm64	NOTE	OK
lme4	r-release-macos-arm64	OK	NOTE
luajr	r-release-macos-arm64	NOTE	OK
magick	r-release-windows-x86_64	ERROR	OK
mantar	r-oldrel-windows-x86_64	ERROR	OK
mantar	r-release-windows-x86_64	ERROR	OK
marsrad	r-release-macos-arm64	NOTE	OK
metadat	r-release-macos-arm64	ERROR	OK
ml	r-release-windows-x86_64	ERROR	OK
mlr3misc	r-release-macos-arm64	OK	ERROR
mlr3pipelines	r-release-windows-x86_64	ERROR	OK
neo4r	r-release-macos-arm64	NOTE	OK
nimble	r-release-macos-arm64	OK	NOTE
orbweaver	r-release-macos-arm64	NOTE	OK
ouladFormat	r-release-windows-x86_64	ERROR	OK
panstarrs	r-release-windows-x86_64	OK	ERROR
parameters	r-release-macos-arm64	ERROR	OK
pillar	r-release-macos-arm64	ERROR	OK
pkgdown	r-release-macos-arm64	ERROR	OK
plmmr	r-release-macos-arm64	WARNING	OK
polite	r-release-macos-arm64	NOTE	OK
portfolioBacktest	r-release-macos-arm64	ERROR	OK
potential	r-oldrel-windows-x86_64	OK	ERROR
pressuRe	r-release-windows-x86_64	ERROR	OK
priceR	r-release-macos-arm64	NOTE	OK
proftools	r-oldrel-windows-x86_64	ERROR	NOTE
profvis	r-release-windows-x86_64	ERROR	OK
promor	r-release-windows-x86_64	ERROR	OK
purrr	r-release-macos-arm64	ERROR	OK
qPRAentry	r-oldrel-windows-x86_64	OK	ERROR
rATTAINS	r-release-macos-arm64	OK	ERROR
rAccess	r-release-windows-x86_64	OK	ERROR
rFIA	r-release-macos-arm64	WARNING	OK
rGhanaCensus	r-release-macos-arm64	ERROR	NOTE
rSpectral	r-release-macos-arm64	ERROR	OK
rTLS	r-oldrel-windows-x86_64	ERROR	OK
rappdirs	r-release-macos-arm64	ERROR	OK
rbm25	r-release-macos-arm64	NOTE	OK
rbranding	r-release-macos-arm64	ERROR	OK
rcldf	r-oldrel-windows-x86_64	OK	ERROR
rcrisp	r-oldrel-windows-x86_64	ERROR	OK
rcrisp	r-release-windows-x86_64	OK	ERROR
readmit	r-release-windows-x86_64	ERROR	OK
restatapi	r-release-macos-arm64	ERROR	OK
rgexf	r-release-macos-arm64	NOTE	OK
rodeo	r-oldrel-windows-x86_64	OK	ERROR
rsi	r-oldrel-windows-x86_64	OK	ERROR
rsolr	r-release-windows-x86_64	ERROR	OK
rstudioapi	r-release-macos-arm64	OK	NOTE
rtiktoken	r-release-macos-arm64	NOTE	OK
scAnnotate	r-oldrel-windows-x86_64	ERROR	OK
scAnnotate	r-release-macos-arm64	ERROR	OK
scAnnotate	r-release-windows-x86_64	ERROR	OK
sdmTMB	r-oldrel-windows-x86_64	OK	ERROR
see	r-release-windows-x86_64	OK	ERROR
sfclust	r-oldrel-windows-x86_64	OK	ERROR
sfislands	r-oldrel-windows-x86_64	ERROR	OK
sfnetworks	r-release-macos-arm64	ERROR	OK
sftrack	r-release-macos-arm64	NOTE	OK
sgapi	r-release-macos-arm64	ERROR	OK
spMaps	r-release-windows-x86_64	ERROR	OK
stars	r-release-windows-x86_64	OK	ERROR
statnet	r-oldrel-windows-x86_64	NOTE	OK
stringr	r-release-macos-arm64	ERROR	OK
survey	r-release-macos-arm64	OK	ERROR
symphony	r-oldrel-windows-x86_64	ERROR	OK
symphony	r-release-macos-arm64	ERROR	OK
symphony	r-release-windows-x86_64	ERROR	OK
tcpl	r-release-macos-arm64	ERROR	OK
telemetR	r-release-macos-arm64	ERROR	OK
telraamStats	r-release-macos-arm64	ERROR	OK
tenm	r-release-macos-arm64	ERROR	OK
tepr	r-oldrel-windows-x86_64	ERROR	OK
test.assessr	r-release-macos-arm64	ERROR	OK
tibble	r-release-windows-x86_64	ERROR	OK
tidypmc	r-oldrel-windows-x86_64	OK	ERROR
tidystats	r-release-macos-arm64	OK	ERROR
tidystringdist	r-release-macos-arm64	NOTE	OK
timeperiodsR	r-release-macos-arm64	ERROR	OK
tongfen	r-release-windows-x86_64	ERROR	OK
treePlotArea	r-release-windows-x86_64	ERROR	OK
tsfeatures	r-release-windows-x86_64	ERROR	OK
usportsR	r-release-macos-arm64	ERROR	OK
vroom	r-release-macos-arm64	OK	NOTE
whSample	r-release-macos-arm64	WARNING	OK
wingen	r-release-windows-x86_64	ERROR	OK
withr	r-release-macos-arm64	ERROR	OK
wrProteo	r-release-macos-arm64	ERROR	OK
xactonomial	r-release-macos-arm64	NOTE	OK
yaml	r-release-macos-arm64	NOTE	OK
ymd	r-release-macos-arm64	NOTE	OK
zoo	r-release-macos-arm64	ERROR	OK
zoomerjoin	r-release-macos-arm64	NOTE	OK

If the machine and R versions is the same but the check of the package is different there might be some discrepancy between the dependencies.

# Extract dependencies
dependencies <- package_dependencies(unique(possible_packages$Package),
                                     # Should it check all the recursive dependencies or only direct?
                                     db = ap, # Only considering those dependencies on CRAN and Bioconductor but not any Additional_repositories. 
                                     recursive = TRUE, 
                                     which = c("Depends", "Imports", "LinkingTo", "Suggests"))

# Prepare to compare versions (as they are sorted by everything else we can compare directly)
intermittent_failures <- rep(FALSE, length(dependencies))
names(intermittent_failures) <- names(dependencies)
dep_0 <- lengths(dependencies) == 0
intermittent_failures[dep_0] <- TRUE

If they do not have any recursive dependency on Depends, Imports, LinkingTo and Suggests they might be have some intermittent problems on the packages. These is only on dependencies on CRAN and Bioconductor but not in other additional repositories (There are 196 packages with additional repositories).

If they have some dependencies and those dependencies didn’t change as far as we can tell then there might be some problems with random numbers or connectivity.

for (pkg in names(intermittent_failures[!intermittent_failures])) {
  dep <- dependencies[[pkg]]
  fl <- possible_packages$Flavor[possible_packages$Package == pkg]
  intermittent_failures[pkg] <- all_checks |> 
    filter(Package %in% dep,
           Flavor %in% fl,
           Version.t == Version.y,
           Status.t != Status.y) |> 
    nrow() == 0 # If packages outside || any(!dep %in% rownames(ap)) 
}
packages <- names(intermittent_failures)[intermittent_failures]

We finally show the differences on the status of those without any dependency change on version or status¹:

keep_files <- filter(possible_packages, Package %in% packages) |> 
  merge(y = flavors_df, by.x = "Flavor", by.y = "flavors", all.x = TRUE, all.y = FALSE) |> 
  select(Package, Flavor, Version = Version.t, R_version = r_version, OS = os, 
         architecture, other, version, revision) |> 
  mutate(Date = Sys.time())

if (nrow(keep_files >= 1)) {
  write.csv(keep_files, 
            paste0("cran-failing-", format(Sys.time(), "%Y%m%dT%H%M"), ".csv"),
            row.names = FALSE,
            quote = FALSE,
  )
}

filter(possible_packages, Package %in% packages) |> 
  select(Package, Flavor, Today, Yesterday, -Version.t, -Version.y) |> 
  flextable() |> 
  autofit()

Package	Flavor	Today	Yesterday
boxcoxmix	r-devel-linux-x86_64-fedora-gcc	ERROR	OK

Conclusion

cat("There are no packages detected with differences between yesterday and today attributable to intermittent failures.\n")
knitr::knit_exit()

cat("This suggests that these packages might have some problems with random numbers or connectivity:\n\n") 

This suggests that these packages might have some problems with random numbers or connectivity:

if (any(dep_0)) {
  cat("\n## Packages with dependencies\n\n")
  cat(paste0(" - ", sort(intersect(packages, 
                                   names(dependencies)[dep_0])), "\n"), sep = "")
  cat("\n## Packages without dependencies\n\n")
  cat(paste0(" - ", sort(intersect(packages,
                                   names(dependencies)[!dep_0])), "\n"), sep = "")
  
} else {
  cat(paste0(" - ", sort(packages), "\n"), sep = "")
}

• boxcoxmix

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1. I think a new version might not propagate to check other packages until 24 hours later as checks might have already started for that day.↩︎