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		r89344
r-devel-linux-x86_64-debian-gcc	devel	linux	x86_64	debian-gcc		r89365
r-devel-linux-x86_64-fedora-clang	devel	linux	x86_64	fedora-clang		r89309
r-devel-linux-x86_64-fedora-gcc	devel	linux	x86_64	fedora-gcc		r89323
r-patched-linux-x86_64	patched	linux	x86_64		4.5.2	r89335
r-release-linux-x86_64	release	linux	x86_64		4.5.2
r-release-macos-arm64	release	macos	arm64		4.5.0
r-release-macos-x86_64	release	macos	x86_64		4.5.1
r-release-windows-x86_64	release	windows	x86_64		4.5.2
r-oldrel-macos-arm64	oldrel	macos	arm64		4.4.3
r-oldrel-macos-x86_64	oldrel	macos	x86_64		4.4.1
r-oldrel-windows-x86_64	oldrel	windows	x86_64		4.4.3

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())

Machines (y axis) vs install time (seconds, x axis), violing plot usually around 10 seconds.

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 65 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())

Machines (y axis) vs check time (seconds, x axis), violing plot usually around 100 seconds.

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 323 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())

Machines (y axis) vs total time (seconds, x axis), violing plot usually around 100 seconds.

Distribution of total time on each machine.

This means that to install and check all the packages with a single CPU would take 401 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 240.44 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	22,700
2	368
3	5

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	22,935
10	39
11	35
12	24
8	17
3	12
9	6
7	5

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())

Flavors of machines and versions of packages

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())

On the vertical axis the machine, on the horitzonal axis the packages colored by the status.

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	packages
13	0	13,089
11	2	4,492
10	3	1,493
0	13	1,153
8	5	817
9	4	321

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 0.60%, 0.59%, 0.05%, 0.04%, 0.00% 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
AutoWMM	r-oldrel-windows-x86_64	OK	ERROR
BDgraph	r-devel-linux-x86_64-fedora-gcc	NOTE	OK
BeeBDC	r-release-linux-x86_64	OK	NOTE
CNVScope	r-oldrel-windows-x86_64	ERROR	NOTE
ChinAPIs	r-devel-linux-x86_64-fedora-clang	ERROR	OK
ChinAPIs	r-devel-linux-x86_64-fedora-gcc	ERROR	OK
ChinAPIs	r-oldrel-windows-x86_64	ERROR	OK
ChinAPIs	r-release-linux-x86_64	ERROR	OK
DATAstudio	r-devel-linux-x86_64-fedora-clang	ERROR	OK
DATAstudio	r-devel-linux-x86_64-fedora-gcc	ERROR	OK
DATAstudio	r-oldrel-windows-x86_64	ERROR	OK
DATAstudio	r-release-linux-x86_64	ERROR	OK
FORTLS	r-oldrel-windows-x86_64	ERROR	NOTE
FORTLS	r-release-linux-x86_64	ERROR	OK
GSEMA	r-oldrel-windows-x86_64	OK	ERROR
MoEClust	r-release-linux-x86_64	OK	NOTE
OmopViewer	r-oldrel-windows-x86_64	ERROR	OK
OmopViewer	r-release-linux-x86_64	ERROR	OK
OptimalBinningWoE	r-devel-linux-x86_64-fedora-clang	OK	WARNING
RSNNS	r-devel-linux-x86_64-fedora-clang	OK	WARNING
RSTr	r-oldrel-windows-x86_64	NOTE	ERROR
RTL	r-devel-linux-x86_64-fedora-clang	OK	WARNING
TreeDist	r-oldrel-windows-x86_64	ERROR	NOTE
TreeDist	r-release-linux-x86_64	ERROR	OK
TrialEmulation	r-release-linux-x86_64	NOTE	OK
aebdata	r-devel-linux-x86_64-fedora-clang	ERROR	OK
aebdata	r-devel-linux-x86_64-fedora-gcc	ERROR	OK
aebdata	r-release-linux-x86_64	ERROR	OK
afex	r-devel-linux-x86_64-fedora-clang	NOTE	OK
afex	r-devel-linux-x86_64-fedora-gcc	NOTE	OK
apa	r-devel-linux-x86_64-fedora-clang	ERROR	OK
apa	r-devel-linux-x86_64-fedora-gcc	ERROR	OK
arkdb	r-oldrel-windows-x86_64	ERROR	OK
arkdb	r-release-linux-x86_64	ERROR	OK
arules	r-release-linux-x86_64	NOTE	OK
autograph	r-oldrel-windows-x86_64	OK	ERROR
bootnet	r-devel-linux-x86_64-fedora-gcc	NOTE	OK
box.lsp	r-release-linux-x86_64	ERROR	OK
brfinance	r-release-linux-x86_64	ERROR	OK
combinIT	r-release-linux-x86_64	OK	ERROR
dataquieR	r-oldrel-windows-x86_64	OK	ERROR
delimtools	r-release-linux-x86_64	OK	NOTE
ecb	r-release-linux-x86_64	OK	ERROR
fNonlinear	r-oldrel-windows-x86_64	NOTE	OK
fNonlinear	r-release-linux-x86_64	NOTE	OK
fastml	r-devel-linux-x86_64-fedora-clang	OK	WARNING
fmeffects	r-devel-linux-x86_64-fedora-clang	OK	ERROR
ipeaplot	r-devel-linux-x86_64-fedora-clang	ERROR	OK
ipeaplot	r-devel-linux-x86_64-fedora-gcc	ERROR	OK
ipeaplot	r-release-linux-x86_64	ERROR	OK
kappalab	r-release-linux-x86_64	ERROR	OK
klassR	r-oldrel-windows-x86_64	ERROR	OK
lgrExtra	r-release-linux-x86_64	OK	NOTE
metabodecon	r-oldrel-windows-x86_64	ERROR	NOTE
nlrx	r-oldrel-windows-x86_64	OK	ERROR
nodbi	r-release-linux-x86_64	OK	NOTE
npreg	r-devel-linux-x86_64-fedora-clang	ERROR	OK
npreg	r-devel-linux-x86_64-fedora-gcc	ERROR	OK
ohsome	r-oldrel-windows-x86_64	OK	NOTE
partykit	r-release-linux-x86_64	ERROR	OK
pcalg	r-devel-linux-x86_64-fedora-gcc	NOTE	OK
pkgdiff	r-release-linux-x86_64	ERROR	OK
pkgndep	r-oldrel-windows-x86_64	OK	ERROR
pmmlTransformations	r-release-linux-x86_64	ERROR	OK
pmparser	r-devel-linux-x86_64-fedora-clang	ERROR	OK
pmparser	r-devel-linux-x86_64-fedora-gcc	ERROR	OK
pmparser	r-oldrel-windows-x86_64	ERROR	OK
pmparser	r-release-linux-x86_64	ERROR	OK
pulsar	r-devel-linux-x86_64-fedora-clang	ERROR	OK
pulsar	r-devel-linux-x86_64-fedora-gcc	ERROR	OK
qgraph	r-devel-linux-x86_64-fedora-gcc	NOTE	OK
qrlabelr	r-oldrel-windows-x86_64	WARNING	OK
qrlabelr	r-release-linux-x86_64	WARNING	NOTE
readr	r-oldrel-windows-x86_64	ERROR	OK
readr	r-release-linux-x86_64	ERROR	OK
rodeo	r-oldrel-windows-x86_64	ERROR	OK
rsconnect	r-oldrel-windows-x86_64	OK	ERROR
scPOEM	r-oldrel-windows-x86_64	ERROR	OK
schoRsch	r-devel-linux-x86_64-fedora-clang	NOTE	OK
schoRsch	r-devel-linux-x86_64-fedora-gcc	NOTE	OK
seekr	r-oldrel-windows-x86_64	ERROR	OK
seekr	r-release-linux-x86_64	ERROR	OK
shiny.reglog	r-oldrel-windows-x86_64	WARNING	OK
shiny.reglog	r-release-linux-x86_64	WARNING	OK
tensorEVD	r-release-linux-x86_64	ERROR	OK
tfrmtbuilder	r-oldrel-windows-x86_64	WARNING	OK
tfrmtbuilder	r-release-linux-x86_64	WARNING	OK
timeplyr	r-devel-linux-x86_64-fedora-clang	OK	ERROR
timeplyr	r-devel-linux-x86_64-fedora-gcc	OK	ERROR
timeplyr	r-oldrel-windows-x86_64	ERROR	OK
timeplyr	r-release-linux-x86_64	ERROR	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 183 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
schoRsch	r-devel-linux-x86_64-fedora-clang	NOTE	OK
schoRsch	r-devel-linux-x86_64-fedora-gcc	NOTE	OK
kappalab	r-release-linux-x86_64	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 = "")
}

kappalab
schoRsch

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.↩︎

Packages intermittent failtures

Lluís Revilla Sancho

2026-02-01